Validation organoid data
Rachel Edgar
2021-10-01
Load Libraries
suppressMessages(library(minfi))
suppressMessages(library(reshape))
suppressMessages(library(ggplot2))
suppressMessages(library(gridExtra))
suppressMessages(library(RColorBrewer))
suppressMessages(library(here))
suppressMessages(library(binom))
suppressMessages(library(limma))
suppressMessages(library(sva))
suppressMessages(library(pamr))
suppressMessages(library(GEOquery))
suppressMessages(library(GEOmetadb))
suppressMessages(library(dplyr))
suppressMessages(library(lmtest))
suppressMessages(library(gridExtra))
suppressMessages(library(gtools))
suppressMessages(library(rafalib))
options(stringsAsFactors = FALSE)Load Functions
source(here("scripts","00_pretty_plots.R"))
suppressMessages(source(here("scripts","00_heat_scree_plot_generic.R")))
source(here("scripts","00_EM_array_uniform_background_maximise_betabinom.R"))Load Data
path<-"data/validation/DNAm"
epic.organoid1<-read.csv(here(path, "METH_K_Nayak_20035_SS_Plate1.csv"), skip=7)
epic.organoid1$plate_path<-paste(epic.organoid1$Sample_Plate,"_96_Samples",sep="")
epic.organoid2<-read.csv(here(path, "METH_K_Nayak_20035_SS_Plate2.csv"), skip=7)
epic.organoid2$plate_path<-paste(epic.organoid2$Sample_Plate,"_96_samples",sep="")
epic.organoid3<-read.csv(here(path, "METH_K_Nayak_20035_SS_Plate3.csv"), skip=7)
epic.organoid3$plate_path<-paste(epic.organoid3$Sample_Plate,"_16_samples",sep="")
epic.organoid<-rbind(epic.organoid1,epic.organoid2,epic.organoid3)add gender
sampleInfo<-read.csv(here("data/validation", "Final samples for submission 2021.csv"))
epic.organoid<-merge(epic.organoid,sampleInfo[c("Sample.Name", "Age", "Diagnosis", "Gender", "GEPadGI", "BOX", "Segment","Source", "Wnt.type","Biobank.Rachel.Replicates")], by.x="Sample_Name", by.y="Sample.Name")
epic.organoid<-epic.organoid[which(epic.organoid$Biobank.Rachel.Replicates=="Rachel"),]Normalize DNAm Arrays
here(path)## [1] "/nfs/research1/zerbino/redgar/DNAm_organoid_passage/data/validation/DNAm"epic.organoid$array.id.path <- file.path(here(path,"Data"),epic.organoid$plate_path, epic.organoid$Sentrix_ID, paste(epic.organoid$Sentrix_ID, epic.organoid$Sentrix_Position, sep="_"))
epic.organoid$array.id<-paste(epic.organoid$Sentrix_ID, epic.organoid$Sentrix_Position, sep="_")
epic.organoid$individual<-sapply(1:nrow(epic.organoid), function(x) strsplit(epic.organoid$Sample_Name[x]," ")[[1]][1])
epic.organoid$passage<-as.numeric(sapply(1:nrow(epic.organoid), function(x) gsub("p","",strsplit(epic.organoid$Sample_Name[x]," ")[[1]][3])))
epic.organoid$passage_hilo<-sapply(1:nrow(epic.organoid), function(x) if(epic.organoid$passage[x]<5){"low"}else{"high"})
epic.organoid$condition<-sapply(1:nrow(epic.organoid), function(x) strsplit(epic.organoid$Sample_Name[x]," ")[[1]][4])
epic.organoid$condition<-as.factor(epic.organoid$condition)
levels(epic.organoid$condition)<-c("D","IFNg","IFNg","TNFa","UD","UT")
epic.organoid$condition<-as.character(epic.organoid$condition)
epic.organoid$comparison<-sapply(1:nrow(epic.organoid), function(x) if(epic.organoid$condition[x]%in%c("UD","D")){"differentiation"}else{"cytokine"})
epic.organoid$treatment<-sapply(1:nrow(epic.organoid), function(x) if(epic.organoid$comparison[x]=="cytokine"){epic.organoid$condition[x]}else{"UT"})
epic.organoid$differentiation<-sapply(1:nrow(epic.organoid), function(x) if(epic.organoid$comparison[x]=="differentiation"){epic.organoid$condition[x]}else{"UD"})
# multiple DMAP files common with epic so need to force https://support.bioconductor.org/p/97773/
rgset_organoid <- read.metharray(epic.organoid$array.id.path, verbose = FALSE,force=TRUE)
# Background and dye bias correction with noob thhrough funnorm implemented in minfi
#http://bioconductor.org/help/course-materials/2015/BioC2015/methylation450k.html
MSet.illumina <- preprocessFunnorm(rgset_organoid, sex=epic.organoid$Gender)## [preprocessFunnorm] Background and dye bias correction with noob## Loading required package: IlluminaHumanMethylationEPICmanifest## Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19## [preprocessFunnorm] Mapping to genome## [preprocessFunnorm] Quantile extraction## [preprocessFunnorm] Normalizationorganoid_beta<-getBeta(MSet.illumina)
print(paste("Samples available: ",ncol(organoid_beta),"; Probes available: ",nrow(organoid_beta),sep=""))## [1] "Samples available: 42; Probes available: 865859"Detection p values across all probes for each sample
avg_detPval <- colMeans(detectionP(rgset_organoid))
epic.organoid$det_pval<-avg_detPval
ggplot(epic.organoid)+geom_boxplot(aes(as.factor(Sentrix_ID), det_pval, fill=as.factor(Sentrix_ID)), outlier.shape = NA)+
geom_point(aes(as.factor(Sentrix_ID), det_pval, group=Sample_Name, fill=as.factor(Sentrix_ID)), shape=21, color="black",
position = position_jitter(w = 0.25))+theme_bw()+theme(axis.text.x=element_text(angle = 45, vjust = 1, hjust=1))+
xlab("Sentrix ID")+ylab("Mean Detection P Value")+guides(fill=FALSE)
ggsave(here("figs","validation_detection_pvalue_organoids.pdf"), width=6, height=5)
ggsave(here("figs/jpeg","validation_detection_pvalue_organoids.jpeg"), width=6, height=5)Beta distribution before and after normalization
# extract raw beta values for plotting
beta_raw<-getBeta(rgset_organoid)
identical(colnames(beta_raw),epic.organoid$array.id)## [1] TRUEBeta_melted<- melt(organoid_beta)
Beta_melted_raw<- melt(beta_raw)
# Remove NAs before plotting (otherwise get many non-inifnite warnings)
Beta_Plot<-Beta_melted[which(!(is.na(Beta_melted$value))),]
Beta_Plot_raw<-Beta_melted_raw[which(!(is.na(Beta_melted_raw$value))),]
# Add meta data
colnames(Beta_Plot)<-c("CpG","ID","Beta")
Beta_Plot<-merge(Beta_Plot,epic.organoid, by.x="ID", by.y="array.id")
colnames(Beta_Plot_raw)<-c("CpG","ID","Beta")
Beta_Plot_raw<-merge(Beta_Plot_raw,epic.organoid, by.x="ID", by.y="array.id")
beta_dis_EPIC_raw<-ggplot(Beta_Plot_raw, aes(Beta, group=as.character(ID), color=as.character(Segment)))+
geom_density()+theme_bw()+colscale_sampsite+xlab("DNAm Beta Value")
beta_dis_EPIC<-ggplot(Beta_Plot, aes(Beta, group=as.character(ID), color=as.character(Segment)))+
geom_density()+theme_bw()+colscale_sampsite+xlab("DNAm Beta Value")
grid.arrange(beta_dis_EPIC_raw,beta_dis_EPIC)
ggsave(here("figs","validation_beta_distribution_organoid.pdf"),grid.arrange(beta_dis_EPIC_raw,beta_dis_EPIC), w=10, h=5)
ggsave(here("figs/jpeg","validation_beta_distribution_organoid.jpeg"),grid.arrange(beta_dis_EPIC_raw,beta_dis_EPIC), w=10, h=5)Confirm individuals ID with SNPs probes and clustering by DNAm
# remove rows with NAs
Betas_cluster<-organoid_beta[complete.cases(organoid_beta),]
d <- dist(t(Betas_cluster))
hc <- hclust(d, method = "complete") #single, complete, average, ward
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(epic.organoid$Segment), cex=1.5)
pdf(here("figs","validation_cluster_wholeEPIC_organoid.pdf"), width=30)
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(epic.organoid$Segment), cex=1.5)
dev.off()## png
## 2Genotyping Probes
SNPs <- getSnpBeta(rgset_organoid)
SNPs<-SNPs[complete.cases(SNPs),]# 65 cause one was all NA
SNPs<-SNPs[,which(colnames(SNPs)%in%epic.organoid$array.id)]
identical(colnames(SNPs),epic.organoid$array.id)## [1] TRUEd <- dist(t(SNPs))
hc <- hclust(d, method = "complete") #single, complete, average, ward
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(as.character(epic.organoid$individual)), cex=1.5)
pdf(here("figs","validation_cluster_snps_EPIC_organoid.pdf"), width=30)
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(as.character(epic.organoid$individual)), cex=1.5)
dev.off()## png
## 2Sex clustering
Using the cg ID to chromosome annotation from illumina https://emea.support.illumina.com/downloads/infinium-methylationepic-v1-0-product-files.html
anno_EPIC<-read.csv(here("data", "MethylationEPIC_v-1-0_B4.csv"), skip=7)
organoid_beta<-organoid_beta[which(rownames(organoid_beta)%in%anno_EPIC$IlmnID),]
anno_EPIC<-anno_EPIC[match(rownames(organoid_beta),anno_EPIC$IlmnID),]
identical(rownames(organoid_beta),anno_EPIC$IlmnID)## [1] TRUEorganoid_beta_sex<-organoid_beta[which(anno_EPIC$CHR%in%c('X','Y')),]
d <- dist(t(organoid_beta_sex))
hc <- hclust(d, method = "complete") #single, complete, average, ward
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(epic.organoid$Gender), cex=1.5)
pdf(here("figs","validation_cluster_sex_EPIC_organoid.pdf"), width=30)
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(epic.organoid$Gender), cex=1.5)
dev.off()## png
## 2Remove samples which do not cluster correctly
none to remove here though ### Probe Filtering
# SNP probes should already be removed
organoid_beta <- organoid_beta[!grepl("rs",rownames(organoid_beta)), ]
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))## [1] "Samples available: 42\nProbes available: 865859"Sex Chromosomes
anno_EPIC<-anno_EPIC[anno_EPIC$IlmnID%in%rownames(organoid_beta),]
identical(rownames(organoid_beta),anno_EPIC$IlmnID)## [1] TRUEorganoid_beta <- organoid_beta[!anno_EPIC$CHR%in%c("X", "Y"), ]
filt_sex<-nrow(organoid_beta)
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))## [1] "Samples available: 42\nProbes available: 846232"Cross-hybridizing probes and polymorphic probes.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1066-1 “43,254 cross-reactive probes with ≥ 47 bp homology with an off-target site, of which 15,782 (36.5 %) are new to the EPIC platform” They include this annotated list in their supplement. wget https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM2_ESM.csv
cross_reactive<-read.csv(here("data", "13059_2016_1066_MOESM2_ESM.csv"), stringsAsFactors = F)
organoid_beta<-organoid_beta[which(!(rownames(organoid_beta)%in%cross_reactive$PROBE)),]
filt_cross<-nrow(organoid_beta)
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))## [1] "Samples available: 42\nProbes available: 814600"For polymorphic probes I will The Pidsley annotation aswell for “Probes overlapping genetic variants at targeted CpG sites.” and “Probes overlapping genetic variants at single base extension sites for Infinium Type I probes” but NOT “Probes with genetic variants overlapping the body of the probe: 48 base pairs for Infinium Type I probes and 49 base pairs for Infinium Type II probes.”
#wget https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM4_ESM.csv
#wget https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM5_ESM.csv
polymorphic<-read.csv(here("data", "13059_2016_1066_MOESM4_ESM.csv"), stringsAsFactors = F)
print(paste("Filtering ",length(unique(polymorphic$PROBE))," polymorphic probes (genetic variants at targeted CpG sites).", sep=""))## [1] "Filtering 12378 polymorphic probes (genetic variants at targeted CpG sites)."baseext<-read.csv(here("data", "13059_2016_1066_MOESM5_ESM.csv"), stringsAsFactors = F)
print(paste("Filtering ",length(unique(baseext$PROBE))," polymorphic probes (single base extension sites for Infinium Type I probes).", sep=""))## [1] "Filtering 413 polymorphic probes (single base extension sites for Infinium Type I probes)."organoid_beta<-organoid_beta[which(!(rownames(organoid_beta)%in%c(polymorphic$PROBE, baseext$PROBE))),]
filt_poly<-nrow(organoid_beta)
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))## [1] "Samples available: 42\nProbes available: 802848"Probe filtering based on detection pvalue and detection over background (NA)
Remove probes with high NA count
na_count_probe <-sapply(1:nrow(organoid_beta), function(y) length(which(is.na(organoid_beta[y,]))))
na_count_probe_good<-which(na_count_probe<(ncol(organoid_beta)*0.05))
organoid_beta<-organoid_beta[na_count_probe_good,]
filt_bead<-nrow(organoid_beta)
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))## [1] "Samples available: 42\nProbes available: 802848"Remove probes with high detection p value across samples, and any samples with many high detection p value probes
detP <- detectionP(rgset_organoid)
detP<-detP[,which(colnames(detP)%in%epic.organoid$array.id)]
identical(colnames(detP),epic.organoid$array.id)## [1] TRUEfailed <- detP>0.05
bad_det_p<-names(which(rowMeans(failed)>0.01))
bad_det_psamp<-names(which(colMeans(failed)>0.01))
organoid_beta<-organoid_beta[which(!(rownames(organoid_beta)%in%bad_det_p)),]
organoid_beta<-organoid_beta[,which(!(colnames(organoid_beta)%in%bad_det_psamp))]
identical(colnames(organoid_beta), as.character(epic.organoid$array.id))## [1] TRUEfilt_detp<-nrow(organoid_beta)
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))## [1] "Samples available: 42\nProbes available: 801072"Probe attrition plot
df<-data.frame(sample_num_remaining=c(866238,865918,865859,filt_sex,filt_cross,filt_poly,filt_bead,filt_detp),
filter=c("EPIC Probe Number","Missing Annotation Data","Removal of SNP Probes",
"Removal of X and Y chromosome probes","Removal of Cross Reactive Probes",
"Removal of Polymorphic Probes", "Removal of Probes with Beadcount <3\nin 5 % of Samples",
"Removal of Probes with 1 % of samples\nwith a detection p-value greater than 0.05"))
df$sample_num_lost<-c(0,sapply(2:nrow(df), function(x) df$sample_num_remaining[x-1]-df$sample_num_remaining[x]))
df$filter<-factor(df$filter, rev(df$filter))
ggplot(df)+
geom_bar(aes(filter,-sample_num_remaining), stat="identity", fill="grey70", color="black")+
geom_bar(aes(filter,sample_num_lost), stat="identity",fill="darkred", color="black")+
geom_text(aes(x=filter, y=-min(sample_num_remaining)/2, label=comma(sample_num_remaining)))+
geom_text(aes(x=filter, y=max(sample_num_lost)/1.5, label=comma(sample_num_lost)))+
geom_hline(yintercept=0)+
coord_flip()+theme_bw()+ylab("")+xlab("")+
theme(axis.line = element_blank(),
axis.ticks = element_blank(),
axis.text.x = element_blank(),
axis.text.y = element_text(colour = "grey20", size=12),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
panel.background = element_blank()) +
scale_x_discrete(position = "top")
ggsave(here("figs","validation_probe_attrition.pdf"), width = 8, height = 3)
ggsave(here("figs/jpeg","validation_probe_attrition.jpeg"), width = 8, height = 3)
epic.organoid<-epic.organoid[,which(!(colnames(epic.organoid)%in%c("array.id.path","plate_path","Biobank.Rachel.Replicates","GEPadGI","BOX","Source","Wnt.type","Sample_Group", "Pool_ID")))]
validation_organoid_beta<-organoid_beta
validation_epic.organoid<-epic.organoid
save(validation_organoid_beta, validation_epic.organoid, file=here("data/validation/DNAm","validation_betas_normalized.RData"))
load(file=here("data/validation/DNAm","validation_betas_normalized.RData"))Principal Component Analysis (PCA)
pca_res <- prcomp(t(validation_organoid_beta))
Loadings<-as.data.frame(pca_res$x)
vars <- pca_res$sdev^2
Importance<-vars/sum(vars)
validation_epic.organoid$Sentrix_ID<-as.factor(as.character(validation_epic.organoid$Sentrix_ID))
meta_categorical <- validation_epic.organoid[, c(3,4, 8,9,11,13,16,17)] # input column numbers in meta that contain categorical variables
meta_continuous <- as.data.frame(validation_epic.organoid[, c(6, 12,18)] ) # input column numbers in meta that contain continuous variables
colnames(meta_categorical) <- c("Plate","Sentrix ID","Gender","Segment","Individual", "passage_hilo", "treatment", "differentiation")
colnames(meta_continuous) <- c( "age","passage_numeric", "det_pval")
ord<-1:length(c(colnames(meta_categorical),colnames(meta_continuous)))
# how far do you want the plot to go?
PCs_to_view<-10
suppressWarnings(heat_scree_plot(Loadings, Importance, 3.3, 1.8))
ggsave(here("figs/validation_heat_scree.pdf"), suppressWarnings(heat_scree_plot(Loadings, Importance, 3.3, 1.8)),width = 9, height = 6)
ggsave(here("figs/jpeg","validation_heat_scree.jpeg"), suppressWarnings(heat_scree_plot(Loadings, Importance, 3.3, 1.8)),width = 9, height = 6)
## PC vs PC plot
Loadings$array.id<-rownames(Loadings)
Loadings_meta<-merge(Loadings, validation_epic.organoid, by="array.id")
ggplot(Loadings_meta, aes(PC1, PC2, fill=Segment))+geom_point(shape=21,size=3, color="black")+theme_bw()+
xlab("PC1 (42%)")+ylab("PC2 (12%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 0.1, 1, 1, "cm"))+
scale_fill_manual(values=c("#1a9850", "cornflowerblue","#e1e1ff","#1347a4","#000192"))
ggsave(here("figs","validation_PC12_site.pdf"), width = 5, height = 4)
ggsave(here("figs/jpeg","validation_PC12_site.jpeg"), width = 5, height = 4)
ggplot(Loadings_meta, aes(PC2, PC3, fill=passage_hilo))+
geom_line(aes(PC2,PC3, group=individual, color=individual))+theme_bw()+
geom_point(shape=21,size=3, color="black")+
scale_color_manual(values=c("#d9d9d9","#525252","#969696","#737373","#bdbdbd"),name="Individual")+
scale_fill_manual(values=c("#3288BD","#D53E4F"), name="Passage")+
xlab("PC2 (12%)")+ylab("PC3 (11%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 1, 1, 1, "cm"))
ggsave(here("figs","validation_PC23_passage.pdf"), width = 5.5, height = 4)
ggsave(here("figs/jpeg","validation_PC23_passage.jpeg"), width = 5.5, height = 4)
ggplot(Loadings_meta, aes(PC2, PC3, fill=treatment, color=differentiation))+geom_point(shape=21,size=3)+
scale_color_manual(values=c("black","white"))+scale_fill_manual(values=c("cornflowerblue","firebrick4","grey80"), name="Treatment")+
theme_bw()+
xlab("PC2 (12%)")+ylab("PC3 (11%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 1, 1, 1, "cm"))
ggsave(here("figs","validation_PC23_condition.pdf"), width = 6, height = 4)
ggsave(here("figs/jpeg","validation_PC23_condtion.jpeg"), width = 6, height = 4)Overall Variance Across most Variable CpGs with Passage
Variation<-function(x) {quantile(x, c(0.9), na.rm=T)[[1]]-quantile(x, c(0.1), na.rm=T)[[1]]}
Mval<-function(beta) log2(beta/(1-beta))
organoid_mval = apply(validation_organoid_beta, 1, Mval)
organoid_mval = as.data.frame(organoid_mval)
organoid_mval = t(organoid_mval)
ref_range_dnam<-sapply(1:nrow(organoid_mval), function(x) Variation(organoid_mval[x,]))
validation_organoid_beta_VeryVariable<-validation_organoid_beta[which(ref_range_dnam>=2.75),]
print(paste("There are ",nrow(validation_organoid_beta_VeryVariable), " variable CpGs (10th-90th quantile range in M value >2.75)",sep=""))## [1] "There are 26784 variable CpGs (10th-90th quantile range in M value >2.75)"dim(validation_organoid_beta_VeryVariable<-validation_organoid_beta[rev(order(ref_range_dnam)),])## [1] 801072 42Include the same number of vairable CpGs as organoids varible. So take the 71384 most variable
dim(validation_organoid_beta_VeryVariable<-validation_organoid_beta_VeryVariable[1:71384 ,])## [1] 71384 42# beta plot variable CpGs
Beta_melted<- melt(validation_organoid_beta_VeryVariable)
Beta_Plot<-Beta_melted[which(!(is.na(Beta_melted$value))),]
colnames(Beta_Plot)<-c("CpG","ID","Beta")
Beta_Plot<-merge(Beta_Plot,validation_epic.organoid, by.x="ID", by.y="array.id")
Beta_Plot$passage.or.numeric.factor <- factor(Beta_Plot$passage, levels = c(12,9,8,4,3,2))
ggplot(Beta_Plot, aes(Beta, color=passage.or.numeric.factor))+
geom_density(size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values=rev(c("#D53E4F", "#F46D43", "#FEE08B", "#ABDDA4","#4CA5B1","#5E4FA2")), name="Passage\nNumber")
ggsave(here("figs/validation_variable_CpGs.pdf"),width = 3.75, height = 2.5)
ggsave(here("figs/jpeg","validation_variable_CpGs.jpeg"), width = 3.75, height = 2.5)
ggplot(Beta_Plot, aes(Beta, color=passage.or.numeric.factor, group=ID))+
geom_density(size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+facet_grid(condition~passage.or.numeric.factor)+
scale_color_manual(values=rev(c("#D53E4F", "#F46D43", "#FEE08B", "#ABDDA4","#4CA5B1","#5E4FA2")), name="Passage\nNumber")
ggplot(Beta_Plot[which(Beta_Plot$differentiation=="UD" & Beta_Plot$treatment=="UT"),], aes(Beta, color=passage.or.numeric.factor))+
geom_density(size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values=rev(c("#D53E4F", "#F46D43", "#FEE08B", "#ABDDA4","#4CA5B1","#5E4FA2")), name="Passage\nNumber")
ggplot()+
geom_density(aes(Beta,color=passage_hilo, group=ID),Beta_Plot, size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values = c ("#9ecae1", "#225ea8", "#081d58"), name="Relative\nPassage\nLevel within\nPatient")+facet_grid(condition~individual)+
th+theme(strip.text = element_text(size = 10), axis.text=element_text(size=4),panel.spacing = unit(0.7, "lines"))+th+
scale_x_continuous(breaks = c(0,0.5,1))
Beta_Plot$ID_nopass<-paste(Beta_Plot$individual, Beta_Plot$Segment,Beta_Plot$condition)
ggplot()+
geom_density(aes(Beta,color=passage_hilo, group=ID),Beta_Plot, size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values = c ("#081d58","#9ecae1"), name="Relative\nPassage\nLevel within\nPatient")+facet_wrap(~ID_nopass)+
th+theme(strip.text = element_text(size = 10), axis.text=element_text(size=4),panel.spacing = unit(0.7, "lines"))+th+
scale_x_continuous(breaks = c(0,0.5,1))
ggsave(here("figs","validation_paired_beta.pdf"),width = 5, height = 2.2)
ggsave(here("figs/jpeg","validation_paired_beta.jpeg"),width = 10, height = 10)
ggplot()+
geom_density(aes(Beta,color=passage.or.numeric.factor, group=ID),Beta_Plot, size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values=rev(c("#D53E4F", "#F46D43", "#FEE08B", "#ABDDA4","#4CA5B1","#5E4FA2")))+facet_wrap(~ID_nopass)+
th+theme(strip.text = element_text(size = 10), axis.text=element_text(size=4),panel.spacing = unit(0.7, "lines"))+th+
scale_x_continuous(breaks = c(0,0.5,1))
Thresholding Trimodality
validation_epic.organoid$thresholded_prior_ratio<-sapply(1:nrow(validation_epic.organoid), function(x){
print(x)
converted<-as.numeric(round(validation_organoid_beta_VeryVariable[,x]*1000,0))
counts<-rep(1000, length(converted))
res = em(converted, counts, .41, .31, .27, 0.01, .1, .1, .90, .03, .5, .05)
passage_threshold_params(converted, counts, res)
})## [1] 1
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -397515.94 0.55 0.25 0.18 0.02 0.15
## [7] 0.07 0.88 0.03 0.51 0.05
## [1] -391627.52 0.58 0.24 0.16 0.02 0.15
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -391311.14 0.60 0.22 0.15 0.03 0.15
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -391271.60 0.61 0.22 0.14 0.04 0.15
## [7] 0.06 0.87 0.03 0.52 0.04
## [1] -391279.02 0.61 0.21 0.13 0.04 0.15
## [7] 0.06 0.86 0.03 0.53 0.04
## [1] 2
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -397366.29 0.54 0.25 0.18 0.02 0.15
## [7] 0.07 0.88 0.03 0.51 0.05
## [1] -391640.40 0.58 0.24 0.16 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.04
## [1] -391333.52 0.60 0.23 0.15 0.03 0.15
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -391300.52 0.61 0.22 0.14 0.04 0.15
## [7] 0.06 0.87 0.03 0.52 0.04
## [1] -391314.51 0.61 0.21 0.14 0.04 0.15
## [7] 0.06 0.87 0.03 0.53 0.04
## [1] -391337.56 0.61 0.21 0.14 0.05 0.14
## [7] 0.06 0.87 0.03 0.53 0.04
## [1] -391359.52 0.61 0.20 0.13 0.05 0.14
## [7] 0.06 0.87 0.03 0.53 0.04
## [1] -391372.26 0.61 0.20 0.13 0.06 0.14
## [7] 0.05 0.87 0.03 0.53 0.04
## [1] -391373.64 0.61 0.20 0.13 0.06 0.14
## [7] 0.05 0.87 0.03 0.53 0.04
## [1] 3
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -399244.49 0.56 0.23 0.19 0.02 0.15
## [7] 0.08 0.88 0.03 0.51 0.05
## [1] -392243.87 0.59 0.21 0.17 0.02 0.16
## [7] 0.07 0.87 0.03 0.52 0.05
## [1] -391647.41 0.61 0.20 0.16 0.03 0.17
## [7] 0.07 0.86 0.03 0.53 0.04
## [1] -391483.96 0.62 0.19 0.16 0.03 0.17
## [7] 0.07 0.86 0.03 0.53 0.04
## [1] -391420.21 0.62 0.18 0.16 0.04 0.17
## [7] 0.07 0.86 0.03 0.54 0.04
## [1] -391392.00 0.62 0.18 0.16 0.04 0.17
## [7] 0.07 0.85 0.03 0.54 0.04
## [1] -391379.20 0.62 0.17 0.16 0.05 0.17
## [7] 0.07 0.85 0.03 0.54 0.04
## [1] -391372.70 0.62 0.17 0.16 0.05 0.16
## [7] 0.07 0.85 0.03 0.55 0.04
## [1] 4
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -398551.07 0.55 0.23 0.20 0.02 0.15
## [7] 0.07 0.88 0.03 0.51 0.05
## [1] -392065.62 0.59 0.21 0.18 0.02 0.16
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -391596.77 0.61 0.19 0.17 0.03 0.17
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -391474.81 0.62 0.19 0.16 0.04 0.17
## [7] 0.07 0.86 0.03 0.53 0.04
## [1] -391423.89 0.62 0.18 0.16 0.04 0.17
## [7] 0.07 0.86 0.03 0.54 0.04
## [1] -391395.66 0.62 0.18 0.16 0.04 0.17
## [7] 0.07 0.86 0.03 0.54 0.04
## [1] -391376.19 0.62 0.17 0.16 0.05 0.17
## [7] 0.07 0.86 0.03 0.54 0.04
## [1] -391359.68 0.62 0.17 0.16 0.05 0.16
## [7] 0.07 0.86 0.03 0.55 0.04
## [1] -391343.96 0.62 0.17 0.16 0.06 0.16
## [7] 0.07 0.86 0.03 0.55 0.04
## [1] -391325.61 0.61 0.17 0.16 0.06 0.16
## [7] 0.06 0.86 0.03 0.55 0.04
## [1] -391303.71 0.61 0.17 0.16 0.07 0.16
## [7] 0.06 0.86 0.03 0.55 0.04
## [1] -391277.80 0.60 0.17 0.16 0.07 0.16
## [7] 0.06 0.86 0.03 0.55 0.05
## [1] -391247.99 0.60 0.17 0.16 0.08 0.16
## [7] 0.06 0.86 0.03 0.55 0.05
## [1] -391214.76 0.59 0.17 0.16 0.08 0.16
## [7] 0.06 0.86 0.03 0.56 0.05
## [1] -391178.90 0.59 0.17 0.16 0.08 0.16
## [7] 0.06 0.86 0.03 0.56 0.05
## [1] -391141.28 0.58 0.17 0.16 0.09 0.15
## [7] 0.06 0.87 0.03 0.56 0.05
## [1] -391102.71 0.58 0.17 0.16 0.09 0.15
## [7] 0.06 0.87 0.03 0.56 0.05
## [1] -391064.15 0.57 0.17 0.16 0.10 0.15
## [7] 0.06 0.87 0.03 0.56 0.05
## [1] -391026.39 0.57 0.18 0.16 0.10 0.15
## [7] 0.06 0.87 0.03 0.56 0.06
## [1] -390990.11 0.56 0.18 0.16 0.10 0.15
## [7] 0.06 0.87 0.03 0.56 0.06
## [1] -390955.86 0.56 0.18 0.16 0.11 0.15
## [7] 0.06 0.87 0.03 0.56 0.06
## [1] -390924.08 0.55 0.18 0.16 0.11 0.15
## [7] 0.06 0.87 0.03 0.56 0.06
## [1] -390895.07 0.55 0.18 0.16 0.12 0.15
## [7] 0.06 0.87 0.03 0.56 0.06
## [1] -390869.01 0.54 0.18 0.16 0.12 0.15
## [7] 0.06 0.87 0.03 0.56 0.07
## [1] -390846.05 0.53 0.18 0.16 0.12 0.15
## [7] 0.06 0.87 0.03 0.56 0.07
## [1] -390826.23 0.53 0.18 0.16 0.13 0.15
## [7] 0.06 0.87 0.03 0.56 0.07
## [1] -390809.51 0.52 0.18 0.16 0.13 0.15
## [7] 0.06 0.87 0.03 0.56 0.07
## [1] -390795.83 0.52 0.18 0.16 0.14 0.15
## [7] 0.05 0.87 0.03 0.56 0.07
## [1] -390785.07 0.51 0.19 0.16 0.14 0.15
## [7] 0.05 0.87 0.03 0.56 0.08
## [1] -390777.10 0.50 0.19 0.16 0.15 0.15
## [7] 0.05 0.87 0.03 0.56 0.08
## [1] 5
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401736.10 0.57 0.26 0.15 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393400.10 0.61 0.24 0.12 0.03 0.16
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -392470.87 0.62 0.23 0.11 0.03 0.16
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392163.86 0.63 0.23 0.11 0.04 0.16
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392045.42 0.63 0.22 0.10 0.04 0.16
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392005.88 0.63 0.22 0.10 0.05 0.16
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391999.88 0.63 0.22 0.10 0.05 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] 6
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403181.16 0.59 0.25 0.14 0.02 0.16
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393624.52 0.62 0.24 0.11 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392548.39 0.64 0.23 0.10 0.03 0.17
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392184.71 0.64 0.22 0.09 0.04 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392038.21 0.64 0.22 0.09 0.05 0.17
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -391983.60 0.64 0.22 0.09 0.05 0.17
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391969.28 0.63 0.22 0.09 0.06 0.17
## [7] 0.06 0.81 0.04 0.54 0.04
## [1] -391968.67 0.62 0.22 0.09 0.07 0.17
## [7] 0.06 0.81 0.04 0.54 0.04
## [1] 7
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -404190.72 0.60 0.24 0.14 0.02 0.16
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393891.24 0.64 0.22 0.11 0.03 0.17
## [7] 0.07 0.84 0.03 0.52 0.04
## [1] -392563.39 0.65 0.21 0.11 0.04 0.18
## [7] 0.07 0.83 0.03 0.53 0.04
## [1] -392120.86 0.65 0.20 0.10 0.04 0.18
## [7] 0.07 0.82 0.03 0.53 0.04
## [1] -391966.08 0.65 0.20 0.10 0.05 0.18
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -391933.91 0.64 0.20 0.10 0.06 0.18
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -391953.46 0.64 0.20 0.10 0.06 0.18
## [7] 0.07 0.80 0.04 0.54 0.04
## [1] -391988.49 0.63 0.20 0.11 0.07 0.18
## [7] 0.07 0.80 0.04 0.55 0.04
## [1] -392018.66 0.62 0.20 0.11 0.08 0.18
## [7] 0.07 0.80 0.04 0.55 0.04
## [1] -392034.98 0.61 0.20 0.11 0.08 0.18
## [7] 0.07 0.79 0.04 0.55 0.04
## [1] -392034.36 0.59 0.21 0.11 0.09 0.18
## [7] 0.07 0.79 0.04 0.55 0.04
## [1] 8
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402715.66 0.58 0.24 0.15 0.02 0.16
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393422.88 0.62 0.23 0.13 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -392383.64 0.63 0.22 0.12 0.03 0.17
## [7] 0.07 0.84 0.03 0.53 0.04
## [1] -392049.59 0.64 0.21 0.12 0.04 0.18
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -391925.07 0.64 0.20 0.12 0.04 0.18
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391886.99 0.63 0.20 0.12 0.05 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -391886.54 0.63 0.20 0.12 0.05 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] 9
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401261.69 0.58 0.21 0.19 0.02 0.16
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -392806.79 0.62 0.18 0.17 0.03 0.18
## [7] 0.08 0.86 0.03 0.52 0.04
## [1] -391920.67 0.64 0.17 0.16 0.03 0.19
## [7] 0.08 0.85 0.03 0.53 0.04
## [1] -391632.83 0.65 0.16 0.16 0.04 0.19
## [7] 0.08 0.85 0.03 0.54 0.04
## [1] -391502.84 0.65 0.15 0.15 0.05 0.19
## [7] 0.08 0.84 0.03 0.54 0.04
## [1] -391434.58 0.64 0.15 0.15 0.06 0.19
## [7] 0.08 0.84 0.03 0.55 0.04
## [1] -391394.46 0.64 0.14 0.16 0.06 0.20
## [7] 0.08 0.84 0.03 0.55 0.04
## [1] -391367.24 0.63 0.14 0.16 0.07 0.20
## [7] 0.08 0.84 0.03 0.55 0.04
## [1] -391345.65 0.62 0.14 0.16 0.07 0.19
## [7] 0.08 0.84 0.03 0.55 0.04
## [1] -391324.99 0.62 0.15 0.16 0.08 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391303.07 0.61 0.15 0.16 0.08 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391279.08 0.60 0.15 0.16 0.09 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391252.94 0.59 0.15 0.16 0.09 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391224.95 0.58 0.15 0.17 0.10 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391195.57 0.57 0.16 0.17 0.10 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391165.37 0.56 0.16 0.17 0.11 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -391134.91 0.55 0.16 0.17 0.11 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -391105.88 0.54 0.16 0.17 0.12 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -391075.56 0.54 0.17 0.17 0.12 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -391046.95 0.53 0.17 0.18 0.13 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -391020.14 0.52 0.17 0.18 0.13 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -390995.03 0.51 0.18 0.18 0.14 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -390971.85 0.50 0.18 0.18 0.14 0.19
## [7] 0.08 0.84 0.03 0.56 0.05
## [1] -390950.61 0.49 0.18 0.18 0.15 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390931.35 0.48 0.18 0.18 0.15 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390914.09 0.47 0.19 0.18 0.16 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390898.81 0.46 0.19 0.19 0.16 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390885.44 0.45 0.19 0.19 0.17 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390873.91 0.44 0.19 0.19 0.17 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390863.90 0.44 0.20 0.19 0.18 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390855.79 0.43 0.20 0.19 0.18 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] 10
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400720.44 0.58 0.20 0.20 0.02 0.17
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -392763.80 0.62 0.17 0.18 0.03 0.19
## [7] 0.08 0.87 0.03 0.52 0.04
## [1] -391942.07 0.64 0.15 0.17 0.04 0.20
## [7] 0.08 0.86 0.03 0.53 0.04
## [1] -391656.08 0.65 0.15 0.16 0.04 0.20
## [7] 0.08 0.86 0.03 0.53 0.04
## [1] -391516.99 0.65 0.14 0.16 0.05 0.21
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -391436.11 0.65 0.14 0.16 0.06 0.21
## [7] 0.08 0.85 0.04 0.55 0.04
## [1] -391381.68 0.64 0.13 0.16 0.06 0.21
## [7] 0.08 0.85 0.04 0.55 0.04
## [1] -391339.68 0.63 0.13 0.16 0.07 0.21
## [7] 0.08 0.85 0.04 0.55 0.04
## [1] -391303.39 0.63 0.13 0.17 0.07 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391270.19 0.62 0.14 0.17 0.08 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391237.85 0.61 0.14 0.17 0.08 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391205.97 0.60 0.14 0.17 0.09 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391174.14 0.59 0.14 0.17 0.09 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391143.01 0.59 0.14 0.17 0.10 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391112.14 0.58 0.15 0.17 0.10 0.21
## [7] 0.08 0.85 0.04 0.57 0.04
## [1] -391082.01 0.57 0.15 0.18 0.11 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -391052.94 0.56 0.15 0.18 0.11 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -391025.10 0.55 0.16 0.18 0.12 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390998.66 0.54 0.16 0.18 0.12 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390973.70 0.53 0.16 0.18 0.13 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390950.37 0.52 0.16 0.18 0.13 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390928.73 0.51 0.17 0.18 0.14 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390908.84 0.51 0.17 0.18 0.14 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390890.72 0.50 0.17 0.19 0.15 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390874.38 0.49 0.18 0.19 0.15 0.21
## [7] 0.08 0.85 0.04 0.57 0.06
## [1] -390859.78 0.48 0.18 0.19 0.15 0.21
## [7] 0.08 0.86 0.04 0.57 0.06
## [1] -390846.90 0.47 0.18 0.19 0.16 0.21
## [7] 0.08 0.86 0.04 0.57 0.06
## [1] -390835.69 0.46 0.18 0.19 0.17 0.21
## [7] 0.08 0.86 0.04 0.57 0.06
## [1] -390826.09 0.45 0.19 0.19 0.17 0.21
## [7] 0.08 0.86 0.03 0.57 0.06
## [1] 11
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400291.39 0.57 0.23 0.19 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -392644.37 0.61 0.21 0.16 0.03 0.17
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -392023.33 0.62 0.19 0.15 0.03 0.18
## [7] 0.07 0.86 0.03 0.52 0.04
## [1] -391857.40 0.63 0.19 0.15 0.04 0.18
## [7] 0.07 0.86 0.03 0.53 0.04
## [1] -391790.60 0.63 0.18 0.14 0.04 0.18
## [7] 0.07 0.85 0.03 0.53 0.04
## [1] -391754.53 0.63 0.18 0.14 0.05 0.18
## [7] 0.07 0.85 0.04 0.53 0.04
## [1] -391728.88 0.63 0.18 0.14 0.05 0.18
## [7] 0.07 0.85 0.04 0.54 0.04
## [1] -391705.90 0.62 0.17 0.14 0.06 0.18
## [7] 0.07 0.85 0.04 0.54 0.04
## [1] -391682.67 0.62 0.17 0.14 0.06 0.18
## [7] 0.07 0.85 0.04 0.54 0.04
## [1] -391656.61 0.61 0.17 0.15 0.07 0.18
## [7] 0.07 0.85 0.04 0.54 0.04
## [1] -391627.05 0.61 0.18 0.15 0.07 0.18
## [7] 0.07 0.85 0.04 0.54 0.04
## [1] -391594.02 0.60 0.18 0.15 0.08 0.18
## [7] 0.07 0.85 0.04 0.55 0.04
## [1] -391557.97 0.59 0.18 0.15 0.08 0.17
## [7] 0.07 0.85 0.04 0.55 0.04
## [1] -391519.20 0.59 0.18 0.15 0.08 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391478.70 0.58 0.18 0.15 0.09 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391436.85 0.57 0.18 0.15 0.09 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391395.22 0.57 0.18 0.15 0.10 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391353.56 0.56 0.18 0.16 0.10 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391313.67 0.55 0.19 0.16 0.11 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391275.93 0.54 0.19 0.16 0.11 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391240.19 0.54 0.19 0.16 0.11 0.17
## [7] 0.06 0.85 0.04 0.55 0.06
## [1] -391206.76 0.53 0.19 0.16 0.12 0.17
## [7] 0.06 0.85 0.04 0.55 0.06
## [1] -391175.85 0.52 0.19 0.16 0.12 0.17
## [7] 0.06 0.85 0.04 0.54 0.06
## [1] -391147.56 0.51 0.20 0.16 0.13 0.17
## [7] 0.06 0.85 0.04 0.54 0.06
## [1] -391121.90 0.51 0.20 0.16 0.13 0.17
## [7] 0.06 0.85 0.04 0.54 0.06
## [1] -391098.86 0.50 0.20 0.16 0.14 0.17
## [7] 0.06 0.85 0.04 0.54 0.06
## [1] -391078.34 0.49 0.20 0.17 0.14 0.17
## [7] 0.06 0.85 0.04 0.54 0.06
## [1] -391058.86 0.48 0.20 0.17 0.15 0.17
## [7] 0.06 0.85 0.04 0.54 0.07
## [1] -391042.37 0.48 0.20 0.17 0.15 0.17
## [7] 0.06 0.85 0.04 0.54 0.07
## [1] -391028.36 0.47 0.21 0.17 0.16 0.17
## [7] 0.06 0.85 0.04 0.54 0.07
## [1] -391016.45 0.46 0.21 0.17 0.16 0.17
## [7] 0.06 0.85 0.04 0.54 0.07
## [1] -391004.70 0.45 0.21 0.17 0.17 0.17
## [7] 0.06 0.85 0.04 0.54 0.07
## [1] -390996.07 0.45 0.21 0.17 0.17 0.17
## [7] 0.06 0.86 0.04 0.54 0.07
## [1] 12
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400398.93 0.58 0.22 0.18 0.02 0.16
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -392994.09 0.61 0.20 0.16 0.03 0.17
## [7] 0.08 0.86 0.03 0.52 0.04
## [1] -392346.60 0.63 0.19 0.15 0.03 0.18
## [7] 0.08 0.86 0.03 0.52 0.04
## [1] -392164.50 0.64 0.18 0.14 0.04 0.18
## [7] 0.08 0.85 0.03 0.53 0.04
## [1] -392090.16 0.64 0.17 0.14 0.05 0.18
## [7] 0.08 0.85 0.03 0.53 0.04
## [1] -392050.33 0.64 0.17 0.14 0.05 0.19
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -392022.23 0.64 0.17 0.14 0.06 0.19
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -391997.27 0.63 0.17 0.14 0.06 0.18
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -391972.55 0.63 0.17 0.14 0.07 0.18
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -391945.82 0.62 0.17 0.14 0.07 0.18
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -391916.61 0.61 0.17 0.14 0.08 0.18
## [7] 0.08 0.85 0.04 0.55 0.04
## [1] -391884.90 0.61 0.17 0.14 0.08 0.18
## [7] 0.08 0.85 0.04 0.55 0.04
## [1] -391851.37 0.60 0.17 0.14 0.09 0.18
## [7] 0.07 0.85 0.04 0.55 0.04
## [1] -391815.84 0.59 0.17 0.15 0.09 0.18
## [7] 0.07 0.85 0.04 0.55 0.04
## [1] -391779.28 0.58 0.17 0.15 0.09 0.18
## [7] 0.07 0.85 0.04 0.55 0.04
## [1] -391741.62 0.58 0.18 0.15 0.10 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391704.48 0.57 0.18 0.15 0.10 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391666.96 0.56 0.18 0.15 0.11 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391631.57 0.55 0.18 0.15 0.11 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391598.07 0.55 0.18 0.15 0.12 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391566.28 0.54 0.19 0.15 0.12 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391536.59 0.53 0.19 0.16 0.13 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391509.12 0.52 0.19 0.16 0.13 0.18
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391483.96 0.52 0.19 0.16 0.13 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391461.14 0.51 0.19 0.16 0.14 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391440.66 0.50 0.20 0.16 0.14 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391422.48 0.49 0.20 0.16 0.15 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391406.56 0.48 0.20 0.16 0.15 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391392.80 0.48 0.20 0.16 0.16 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391381.12 0.47 0.20 0.17 0.16 0.17
## [7] 0.07 0.85 0.04 0.55 0.07
## [1] -391371.06 0.46 0.20 0.17 0.17 0.17
## [7] 0.07 0.85 0.04 0.55 0.07
## [1] -391360.75 0.45 0.21 0.17 0.17 0.17
## [7] 0.07 0.85 0.04 0.54 0.07
## [1] -391353.90 0.44 0.21 0.17 0.18 0.17
## [7] 0.07 0.85 0.04 0.54 0.07
## [1] 13
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403138.89 0.59 0.23 0.16 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -393726.11 0.63 0.20 0.14 0.03 0.17
## [7] 0.08 0.85 0.03 0.52 0.05
## [1] -392454.83 0.65 0.19 0.13 0.03 0.18
## [7] 0.08 0.83 0.03 0.53 0.04
## [1] -392029.12 0.65 0.18 0.13 0.04 0.18
## [7] 0.08 0.83 0.04 0.54 0.04
## [1] -391881.03 0.65 0.18 0.13 0.05 0.18
## [7] 0.08 0.82 0.04 0.54 0.04
## [1] -391849.05 0.65 0.17 0.13 0.05 0.18
## [7] 0.08 0.82 0.04 0.54 0.04
## [1] -391863.32 0.64 0.17 0.13 0.06 0.18
## [7] 0.08 0.81 0.04 0.55 0.04
## [1] -391889.93 0.63 0.17 0.13 0.06 0.18
## [7] 0.07 0.81 0.04 0.55 0.04
## [1] -391911.78 0.62 0.17 0.13 0.07 0.18
## [7] 0.07 0.81 0.04 0.55 0.04
## [1] -391921.40 0.61 0.17 0.14 0.07 0.18
## [7] 0.07 0.81 0.04 0.55 0.04
## [1] 14
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403611.87 0.60 0.22 0.16 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -393996.17 0.64 0.20 0.13 0.03 0.18
## [7] 0.08 0.85 0.03 0.52 0.04
## [1] -392661.94 0.65 0.19 0.12 0.04 0.18
## [7] 0.08 0.83 0.04 0.53 0.04
## [1] -392206.40 0.66 0.18 0.12 0.04 0.19
## [7] 0.08 0.83 0.04 0.53 0.04
## [1] -392045.57 0.66 0.17 0.12 0.05 0.19
## [7] 0.08 0.82 0.04 0.54 0.04
## [1] -392008.21 0.65 0.17 0.12 0.06 0.19
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] -392020.53 0.64 0.17 0.12 0.06 0.19
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] -392046.43 0.64 0.17 0.13 0.07 0.19
## [7] 0.08 0.81 0.04 0.55 0.04
## [1] -392067.83 0.63 0.17 0.13 0.07 0.19
## [7] 0.08 0.80 0.04 0.55 0.04
## [1] -392077.62 0.62 0.17 0.13 0.08 0.19
## [7] 0.08 0.80 0.04 0.55 0.04
## [1] 15
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403588.34 0.60 0.24 0.14 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -394220.97 0.64 0.22 0.12 0.03 0.18
## [7] 0.08 0.85 0.03 0.52 0.04
## [1] -393021.13 0.65 0.20 0.11 0.04 0.18
## [7] 0.08 0.83 0.04 0.52 0.04
## [1] -392593.88 0.66 0.20 0.10 0.04 0.19
## [7] 0.08 0.83 0.04 0.53 0.04
## [1] -392423.11 0.66 0.19 0.10 0.05 0.19
## [7] 0.08 0.82 0.04 0.53 0.04
## [1] -392365.42 0.65 0.19 0.10 0.06 0.19
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] -392358.77 0.65 0.19 0.10 0.06 0.19
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] 16
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403501.55 0.60 0.23 0.15 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -394218.47 0.64 0.21 0.12 0.03 0.18
## [7] 0.08 0.85 0.03 0.52 0.04
## [1] -393033.25 0.65 0.20 0.11 0.04 0.19
## [7] 0.08 0.84 0.04 0.52 0.04
## [1] -392617.32 0.66 0.19 0.10 0.04 0.19
## [7] 0.08 0.83 0.04 0.53 0.04
## [1] -392452.85 0.66 0.19 0.10 0.05 0.19
## [7] 0.08 0.82 0.04 0.53 0.04
## [1] -392398.02 0.65 0.19 0.10 0.06 0.19
## [7] 0.08 0.82 0.04 0.54 0.04
## [1] -392392.35 0.65 0.19 0.10 0.06 0.19
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] 17
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -399928.06 0.57 0.19 0.22 0.02 0.16
## [7] 0.09 0.87 0.03 0.51 0.05
## [1] -392356.74 0.61 0.15 0.21 0.03 0.18
## [7] 0.09 0.86 0.03 0.53 0.05
## [1] -391316.08 0.63 0.14 0.20 0.03 0.19
## [7] 0.09 0.85 0.03 0.54 0.04
## [1] -390938.56 0.63 0.12 0.20 0.04 0.20
## [7] 0.10 0.85 0.03 0.54 0.04
## [1] -390775.20 0.63 0.12 0.20 0.04 0.20
## [7] 0.10 0.85 0.03 0.55 0.04
## [1] -390704.67 0.63 0.11 0.21 0.05 0.20
## [7] 0.10 0.84 0.04 0.56 0.04
## [1] -390676.38 0.63 0.11 0.21 0.05 0.21
## [7] 0.10 0.84 0.04 0.56 0.04
## [1] -390665.19 0.62 0.11 0.21 0.06 0.21
## [7] 0.10 0.84 0.04 0.56 0.04
## [1] -390658.34 0.61 0.11 0.21 0.06 0.21
## [7] 0.10 0.84 0.04 0.56 0.04
## [1] 18
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -398969.63 0.57 0.18 0.23 0.02 0.16
## [7] 0.09 0.87 0.03 0.51 0.05
## [1] -392350.42 0.61 0.15 0.22 0.03 0.18
## [7] 0.09 0.86 0.03 0.53 0.04
## [1] -391393.38 0.63 0.13 0.21 0.03 0.19
## [7] 0.10 0.86 0.03 0.54 0.04
## [1] -391026.20 0.63 0.12 0.21 0.04 0.20
## [7] 0.10 0.85 0.03 0.54 0.04
## [1] -390857.04 0.63 0.11 0.21 0.04 0.20
## [7] 0.11 0.85 0.04 0.55 0.04
## [1] -390775.81 0.63 0.11 0.21 0.05 0.20
## [7] 0.11 0.85 0.04 0.56 0.04
## [1] -390735.21 0.63 0.11 0.21 0.05 0.21
## [7] 0.11 0.85 0.04 0.56 0.04
## [1] -390711.63 0.62 0.10 0.21 0.06 0.21
## [7] 0.11 0.85 0.04 0.56 0.04
## [1] -390692.85 0.62 0.10 0.22 0.06 0.21
## [7] 0.11 0.85 0.04 0.56 0.04
## [1] -390673.80 0.61 0.10 0.22 0.07 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390651.64 0.61 0.10 0.22 0.07 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390625.77 0.60 0.11 0.22 0.07 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390596.83 0.59 0.11 0.22 0.08 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390565.71 0.59 0.11 0.22 0.08 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390533.05 0.58 0.11 0.22 0.09 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390499.48 0.58 0.11 0.22 0.09 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390465.59 0.57 0.11 0.22 0.09 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390431.78 0.56 0.12 0.23 0.10 0.20
## [7] 0.11 0.85 0.04 0.58 0.05
## [1] -390398.38 0.56 0.12 0.23 0.10 0.20
## [7] 0.11 0.85 0.04 0.58 0.05
## [1] -390365.66 0.55 0.12 0.23 0.10 0.20
## [7] 0.11 0.85 0.04 0.58 0.05
## [1] -390333.75 0.55 0.12 0.23 0.11 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390302.78 0.54 0.12 0.23 0.11 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390272.89 0.53 0.13 0.23 0.11 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390244.14 0.53 0.13 0.23 0.12 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390216.59 0.52 0.13 0.23 0.12 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390190.28 0.51 0.13 0.23 0.12 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390165.23 0.51 0.13 0.23 0.13 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390141.49 0.50 0.14 0.23 0.13 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390118.97 0.50 0.14 0.23 0.13 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390097.75 0.49 0.14 0.23 0.14 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390077.78 0.48 0.14 0.23 0.14 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390059.02 0.48 0.14 0.23 0.14 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390041.47 0.47 0.15 0.23 0.15 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390025.10 0.46 0.15 0.24 0.15 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390009.88 0.46 0.15 0.24 0.16 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -389995.77 0.45 0.15 0.24 0.16 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -389982.74 0.45 0.15 0.24 0.16 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -389970.76 0.44 0.16 0.24 0.17 0.20
## [7] 0.10 0.85 0.04 0.58 0.07
## [1] -389959.79 0.43 0.16 0.24 0.17 0.20
## [7] 0.10 0.85 0.04 0.58 0.07
## [1] -389949.80 0.43 0.16 0.24 0.17 0.20
## [7] 0.10 0.85 0.04 0.58 0.07
## [1] 19
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -399597.90 0.57 0.21 0.21 0.02 0.16
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -392507.68 0.61 0.18 0.19 0.03 0.17
## [7] 0.08 0.86 0.03 0.52 0.05
## [1] -391710.23 0.62 0.16 0.18 0.03 0.18
## [7] 0.08 0.86 0.03 0.53 0.04
## [1] -391450.54 0.63 0.15 0.18 0.04 0.18
## [7] 0.08 0.85 0.03 0.54 0.04
## [1] -391342.43 0.63 0.15 0.18 0.04 0.18
## [7] 0.09 0.85 0.03 0.54 0.04
## [1] -391295.44 0.63 0.14 0.18 0.05 0.19
## [7] 0.09 0.85 0.03 0.55 0.04
## [1] -391276.18 0.63 0.14 0.18 0.05 0.19
## [7] 0.09 0.85 0.04 0.55 0.04
## [1] -391269.00 0.62 0.14 0.18 0.06 0.18
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] 20
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400914.74 0.58 0.20 0.20 0.02 0.16
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -392712.31 0.62 0.18 0.18 0.03 0.18
## [7] 0.08 0.86 0.03 0.52 0.04
## [1] -391819.32 0.63 0.16 0.17 0.03 0.19
## [7] 0.08 0.85 0.03 0.53 0.04
## [1] -391531.20 0.64 0.15 0.17 0.04 0.19
## [7] 0.08 0.85 0.03 0.54 0.04
## [1] -391407.01 0.64 0.15 0.17 0.05 0.20
## [7] 0.08 0.85 0.03 0.54 0.04
## [1] -391347.36 0.64 0.14 0.17 0.05 0.20
## [7] 0.08 0.85 0.03 0.55 0.04
## [1] -391316.93 0.63 0.14 0.17 0.06 0.20
## [7] 0.08 0.84 0.03 0.55 0.04
## [1] -391299.60 0.63 0.14 0.17 0.06 0.20
## [7] 0.08 0.84 0.03 0.56 0.04
## [1] -391287.10 0.62 0.14 0.17 0.07 0.20
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391275.59 0.61 0.14 0.17 0.07 0.20
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391262.07 0.61 0.15 0.17 0.08 0.20
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391245.40 0.60 0.15 0.17 0.08 0.20
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391225.64 0.59 0.15 0.18 0.09 0.20
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391203.00 0.58 0.15 0.18 0.09 0.20
## [7] 0.08 0.84 0.04 0.57 0.04
## [1] -391177.94 0.57 0.15 0.18 0.09 0.20
## [7] 0.08 0.84 0.04 0.57 0.04
## [1] -391152.52 0.57 0.16 0.18 0.10 0.20
## [7] 0.08 0.84 0.04 0.57 0.04
## [1] -391123.76 0.56 0.16 0.18 0.10 0.20
## [7] 0.08 0.84 0.04 0.57 0.04
## [1] -391094.77 0.55 0.16 0.18 0.11 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -391065.76 0.54 0.17 0.18 0.11 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -391037.17 0.53 0.17 0.19 0.11 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -391009.32 0.52 0.17 0.19 0.12 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -390982.50 0.52 0.17 0.19 0.12 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -390956.89 0.51 0.18 0.19 0.13 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -390932.64 0.50 0.18 0.19 0.13 0.20
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390909.87 0.49 0.18 0.19 0.14 0.20
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390888.60 0.48 0.19 0.19 0.14 0.20
## [7] 0.08 0.85 0.03 0.57 0.05
## [1] -390868.86 0.47 0.19 0.19 0.14 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390850.63 0.47 0.19 0.19 0.15 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390833.89 0.46 0.19 0.20 0.15 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390818.59 0.45 0.20 0.20 0.16 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390804.67 0.44 0.20 0.20 0.16 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390792.09 0.43 0.20 0.20 0.17 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390780.76 0.42 0.20 0.20 0.17 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390770.64 0.42 0.21 0.20 0.18 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390761.67 0.41 0.21 0.20 0.18 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] 21
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403647.99 0.60 0.24 0.14 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -393801.07 0.64 0.22 0.12 0.03 0.17
## [7] 0.08 0.84 0.03 0.52 0.04
## [1] -392537.71 0.65 0.21 0.11 0.04 0.18
## [7] 0.08 0.83 0.03 0.53 0.04
## [1] -392095.16 0.65 0.20 0.10 0.04 0.18
## [7] 0.08 0.82 0.03 0.53 0.04
## [1] -391922.77 0.65 0.19 0.10 0.05 0.18
## [7] 0.08 0.81 0.03 0.54 0.04
## [1] -391869.92 0.65 0.19 0.10 0.06 0.18
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] -391870.44 0.64 0.19 0.11 0.07 0.18
## [7] 0.08 0.80 0.04 0.54 0.04
## [1] 22
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402847.53 0.59 0.24 0.15 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -393886.15 0.63 0.22 0.12 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392760.66 0.64 0.21 0.11 0.03 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392377.06 0.65 0.20 0.11 0.04 0.18
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392231.32 0.65 0.20 0.11 0.05 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392186.68 0.64 0.19 0.11 0.05 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392185.73 0.64 0.19 0.11 0.06 0.18
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] 23
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402801.75 0.59 0.23 0.16 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393639.57 0.63 0.21 0.14 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -392551.37 0.64 0.20 0.13 0.03 0.18
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392180.72 0.65 0.19 0.12 0.04 0.18
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392033.78 0.65 0.19 0.12 0.05 0.18
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391983.12 0.64 0.19 0.12 0.05 0.18
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391975.93 0.64 0.18 0.12 0.06 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] 24
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -404177.72 0.60 0.23 0.15 0.02 0.17
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -394036.85 0.64 0.21 0.12 0.03 0.18
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -392802.68 0.65 0.20 0.11 0.04 0.19
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392371.97 0.66 0.20 0.10 0.04 0.20
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392191.99 0.65 0.19 0.10 0.05 0.20
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392121.30 0.65 0.19 0.10 0.06 0.20
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392101.50 0.64 0.19 0.10 0.06 0.20
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -392102.06 0.63 0.19 0.10 0.07 0.20
## [7] 0.07 0.81 0.05 0.54 0.04
## [1] 25
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -404482.56 0.61 0.23 0.14 0.02 0.17
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393990.92 0.64 0.21 0.12 0.03 0.18
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392686.41 0.66 0.20 0.11 0.04 0.19
## [7] 0.07 0.83 0.03 0.52 0.04
## [1] -392220.64 0.66 0.19 0.10 0.05 0.19
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392024.59 0.66 0.19 0.10 0.05 0.20
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -391949.61 0.65 0.19 0.10 0.06 0.20
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -391931.37 0.64 0.19 0.10 0.07 0.20
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -391935.15 0.63 0.19 0.10 0.08 0.20
## [7] 0.07 0.80 0.04 0.54 0.04
## [1] 26
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402869.78 0.59 0.26 0.14 0.02 0.15
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393897.60 0.62 0.24 0.11 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -392820.30 0.64 0.23 0.10 0.03 0.17
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392440.62 0.64 0.22 0.10 0.04 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392283.37 0.64 0.22 0.09 0.05 0.17
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392225.56 0.64 0.22 0.09 0.05 0.17
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392214.34 0.63 0.22 0.09 0.06 0.17
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -392221.30 0.63 0.22 0.10 0.06 0.17
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] 27
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403547.91 0.59 0.25 0.14 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393838.80 0.63 0.23 0.11 0.03 0.18
## [7] 0.07 0.85 0.03 0.51 0.04
## [1] -392779.46 0.64 0.22 0.10 0.03 0.18
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392404.66 0.65 0.22 0.10 0.04 0.18
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392235.20 0.65 0.21 0.09 0.05 0.18
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392157.19 0.64 0.21 0.09 0.05 0.18
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392124.18 0.64 0.21 0.09 0.06 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392111.11 0.63 0.21 0.09 0.07 0.18
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -392103.47 0.62 0.21 0.10 0.07 0.18
## [7] 0.07 0.81 0.05 0.54 0.04
## [1] 28
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403985.93 0.60 0.25 0.14 0.02 0.16
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393904.32 0.63 0.23 0.11 0.03 0.18
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392759.65 0.64 0.22 0.10 0.03 0.18
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392357.65 0.65 0.22 0.09 0.04 0.19
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392183.66 0.65 0.21 0.09 0.05 0.19
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392111.90 0.64 0.21 0.09 0.06 0.19
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392090.00 0.64 0.21 0.09 0.06 0.19
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -392089.45 0.63 0.21 0.09 0.07 0.19
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] 29
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402127.58 0.58 0.25 0.15 0.02 0.15
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -393953.50 0.62 0.24 0.12 0.03 0.17
## [7] 0.07 0.85 0.04 0.52 0.05
## [1] -392980.52 0.64 0.22 0.11 0.03 0.17
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392629.74 0.64 0.22 0.10 0.04 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392477.38 0.64 0.21 0.10 0.05 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392413.92 0.64 0.21 0.10 0.05 0.17
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392392.53 0.64 0.21 0.10 0.06 0.17
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392388.13 0.63 0.21 0.10 0.06 0.17
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] 30
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403506.10 0.60 0.24 0.14 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -394385.31 0.63 0.22 0.11 0.03 0.18
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -393241.12 0.65 0.21 0.10 0.04 0.18
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392817.30 0.65 0.21 0.10 0.04 0.19
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392632.00 0.65 0.20 0.09 0.05 0.19
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392557.26 0.65 0.20 0.09 0.06 0.19
## [7] 0.07 0.82 0.05 0.54 0.04
## [1] -392536.92 0.65 0.20 0.09 0.06 0.19
## [7] 0.07 0.81 0.05 0.54 0.04
## [1] -392540.01 0.64 0.20 0.09 0.07 0.19
## [7] 0.07 0.81 0.05 0.54 0.04
## [1] 31
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403240.20 0.59 0.23 0.16 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393403.63 0.63 0.21 0.14 0.03 0.18
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -392255.93 0.64 0.19 0.13 0.03 0.18
## [7] 0.07 0.84 0.03 0.53 0.04
## [1] -391885.38 0.64 0.19 0.13 0.04 0.19
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -391746.01 0.64 0.18 0.13 0.05 0.19
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391699.79 0.64 0.18 0.13 0.05 0.19
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -391693.22 0.63 0.18 0.13 0.06 0.19
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] 32
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402911.87 0.59 0.23 0.17 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393714.80 0.62 0.21 0.14 0.03 0.18
## [7] 0.07 0.85 0.04 0.52 0.05
## [1] -392592.72 0.64 0.19 0.13 0.03 0.18
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392230.87 0.65 0.19 0.13 0.04 0.19
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392097.95 0.65 0.18 0.13 0.04 0.19
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392055.26 0.64 0.18 0.13 0.05 0.19
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -392049.02 0.64 0.18 0.13 0.05 0.19
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] 33
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403904.05 0.59 0.20 0.18 0.02 0.18
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393101.84 0.63 0.19 0.16 0.03 0.20
## [7] 0.06 0.86 0.04 0.51 0.05
## [1] -391934.01 0.64 0.18 0.15 0.03 0.21
## [7] 0.06 0.85 0.04 0.52 0.05
## [1] -391592.67 0.64 0.18 0.14 0.04 0.22
## [7] 0.06 0.85 0.04 0.52 0.05
## [1] -391470.08 0.64 0.18 0.14 0.04 0.22
## [7] 0.06 0.84 0.04 0.53 0.04
## [1] -391426.83 0.63 0.18 0.14 0.05 0.22
## [7] 0.06 0.84 0.04 0.53 0.04
## [1] -391416.24 0.63 0.18 0.15 0.05 0.22
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391418.69 0.62 0.18 0.15 0.06 0.22
## [7] 0.06 0.83 0.05 0.54 0.04
## [1] 34
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401732.65 0.57 0.26 0.15 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393375.68 0.61 0.24 0.12 0.03 0.16
## [7] 0.07 0.85 0.03 0.51 0.04
## [1] -392550.12 0.63 0.23 0.11 0.03 0.17
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -392288.08 0.63 0.22 0.11 0.04 0.17
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392178.39 0.63 0.22 0.10 0.04 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392127.30 0.63 0.22 0.10 0.05 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392100.32 0.63 0.22 0.10 0.05 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392081.06 0.62 0.21 0.10 0.06 0.16
## [7] 0.06 0.83 0.04 0.53 0.04
## [1] -392061.05 0.62 0.21 0.10 0.06 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -392035.34 0.61 0.22 0.10 0.07 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] -392002.17 0.60 0.22 0.11 0.07 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] -391961.38 0.60 0.22 0.11 0.08 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391913.76 0.59 0.22 0.11 0.08 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391860.69 0.58 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.05
## [1] -391803.96 0.58 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.05
## [1] -391744.88 0.57 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.05
## [1] -391685.00 0.56 0.22 0.12 0.10 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391625.54 0.55 0.22 0.12 0.10 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391567.42 0.55 0.23 0.12 0.11 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391511.57 0.54 0.23 0.12 0.11 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391458.00 0.53 0.23 0.12 0.12 0.16
## [7] 0.06 0.82 0.05 0.53 0.06
## [1] -391407.30 0.52 0.23 0.12 0.12 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391359.62 0.52 0.23 0.13 0.12 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391314.99 0.51 0.23 0.13 0.13 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391273.38 0.50 0.24 0.13 0.13 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391234.68 0.49 0.24 0.13 0.14 0.15
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391198.76 0.49 0.24 0.13 0.14 0.15
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391165.49 0.48 0.24 0.14 0.15 0.15
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391134.70 0.47 0.24 0.14 0.15 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391106.23 0.46 0.24 0.14 0.16 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391079.92 0.45 0.24 0.14 0.16 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391055.63 0.45 0.25 0.14 0.17 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391033.23 0.44 0.25 0.15 0.17 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391012.57 0.43 0.25 0.15 0.18 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -390993.55 0.42 0.25 0.15 0.18 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -390976.05 0.41 0.25 0.15 0.18 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -390959.97 0.41 0.25 0.15 0.19 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390945.22 0.40 0.25 0.15 0.19 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390931.72 0.39 0.25 0.16 0.20 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390919.39 0.38 0.25 0.16 0.20 0.15
## [7] 0.05 0.82 0.05 0.50 0.08
## [1] -390908.16 0.38 0.26 0.16 0.21 0.15
## [7] 0.05 0.82 0.05 0.50 0.08
## [1] -390897.97 0.37 0.26 0.16 0.21 0.15
## [7] 0.05 0.82 0.05 0.50 0.08
## [1] -390888.75 0.36 0.26 0.16 0.22 0.15
## [7] 0.05 0.82 0.05 0.50 0.08
## [1] 35
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401850.66 0.57 0.25 0.16 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393221.70 0.61 0.23 0.13 0.03 0.17
## [7] 0.07 0.86 0.03 0.52 0.05
## [1] -392372.99 0.62 0.22 0.12 0.03 0.17
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -392119.38 0.63 0.22 0.12 0.04 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392022.92 0.63 0.21 0.12 0.04 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -391985.13 0.63 0.21 0.11 0.05 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -391970.90 0.63 0.21 0.11 0.05 0.17
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391964.31 0.62 0.21 0.12 0.06 0.17
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] 36
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401823.48 0.57 0.25 0.15 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393352.60 0.61 0.24 0.12 0.03 0.17
## [7] 0.07 0.86 0.04 0.51 0.04
## [1] -392519.40 0.62 0.23 0.11 0.03 0.17
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -392268.86 0.63 0.23 0.11 0.04 0.17
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392172.95 0.63 0.22 0.10 0.04 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392134.47 0.63 0.22 0.10 0.05 0.17
## [7] 0.06 0.83 0.04 0.53 0.04
## [1] -392118.38 0.63 0.22 0.10 0.05 0.17
## [7] 0.06 0.83 0.04 0.53 0.04
## [1] -392108.20 0.62 0.22 0.10 0.06 0.17
## [7] 0.06 0.83 0.04 0.53 0.04
## [1] -392095.12 0.62 0.22 0.10 0.06 0.17
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -392074.93 0.61 0.22 0.11 0.07 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] -392046.15 0.60 0.22 0.11 0.07 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] -392008.87 0.60 0.22 0.11 0.08 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] -391964.11 0.59 0.22 0.11 0.08 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391913.38 0.58 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391858.64 0.58 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391801.12 0.57 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.05
## [1] -391742.47 0.56 0.22 0.12 0.10 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391683.95 0.55 0.23 0.12 0.10 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391626.52 0.55 0.23 0.12 0.11 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391571.13 0.54 0.23 0.12 0.11 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391517.83 0.53 0.23 0.12 0.11 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391467.22 0.52 0.23 0.13 0.12 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391419.47 0.52 0.23 0.13 0.12 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391374.65 0.51 0.24 0.13 0.13 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391332.73 0.50 0.24 0.13 0.13 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391293.63 0.49 0.24 0.13 0.13 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391257.24 0.49 0.24 0.13 0.14 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391223.42 0.48 0.24 0.14 0.14 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391192.01 0.47 0.24 0.14 0.15 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391162.88 0.46 0.25 0.14 0.15 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391135.87 0.46 0.25 0.14 0.16 0.16
## [7] 0.06 0.82 0.05 0.52 0.07
## [1] -391110.84 0.45 0.25 0.14 0.16 0.16
## [7] 0.06 0.82 0.05 0.52 0.07
## [1] -391087.66 0.44 0.25 0.15 0.16 0.16
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391066.18 0.43 0.25 0.15 0.17 0.16
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391046.31 0.43 0.25 0.15 0.17 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -391027.93 0.42 0.25 0.15 0.18 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -391010.93 0.41 0.25 0.15 0.18 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -390995.24 0.40 0.26 0.15 0.19 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -390980.76 0.40 0.26 0.16 0.19 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -390967.43 0.39 0.26 0.16 0.20 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390955.16 0.38 0.26 0.16 0.20 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390943.90 0.37 0.26 0.16 0.21 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390933.58 0.37 0.26 0.16 0.21 0.15
## [7] 0.05 0.83 0.05 0.51 0.08
## [1] -390924.16 0.36 0.26 0.16 0.21 0.15
## [7] 0.05 0.83 0.05 0.51 0.08
## [1] 37
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401646.97 0.58 0.23 0.17 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -392856.08 0.61 0.21 0.15 0.03 0.17
## [7] 0.07 0.86 0.03 0.52 0.05
## [1] -391939.60 0.63 0.20 0.14 0.03 0.17
## [7] 0.07 0.85 0.03 0.53 0.04
## [1] -391634.20 0.63 0.19 0.14 0.04 0.17
## [7] 0.07 0.84 0.03 0.53 0.04
## [1] -391506.99 0.63 0.18 0.14 0.04 0.17
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391455.22 0.63 0.18 0.14 0.05 0.17
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391438.02 0.63 0.18 0.14 0.05 0.17
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391434.36 0.62 0.18 0.14 0.06 0.17
## [7] 0.07 0.83 0.04 0.55 0.04
## [1] 38
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402091.04 0.58 0.23 0.17 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -392947.65 0.62 0.21 0.14 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -391982.95 0.63 0.20 0.14 0.03 0.17
## [7] 0.07 0.84 0.03 0.53 0.04
## [1] -391665.86 0.64 0.19 0.13 0.04 0.17
## [7] 0.07 0.84 0.03 0.53 0.04
## [1] -391536.11 0.64 0.19 0.13 0.04 0.17
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391485.04 0.63 0.18 0.13 0.05 0.17
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391469.83 0.63 0.18 0.13 0.06 0.17
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391468.32 0.62 0.18 0.14 0.06 0.17
## [7] 0.07 0.83 0.04 0.55 0.04
## [1] 39
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400190.16 0.56 0.24 0.18 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -392404.48 0.59 0.22 0.16 0.02 0.16
## [7] 0.07 0.86 0.03 0.52 0.05
## [1] -391577.56 0.61 0.21 0.16 0.03 0.16
## [7] 0.07 0.85 0.03 0.53 0.05
## [1] -391319.07 0.62 0.20 0.15 0.03 0.16
## [7] 0.07 0.85 0.03 0.54 0.04
## [1] -391227.25 0.62 0.19 0.15 0.04 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391205.47 0.62 0.19 0.15 0.04 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391214.81 0.61 0.19 0.15 0.05 0.15
## [7] 0.06 0.84 0.04 0.55 0.04
## [1] 40
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400741.31 0.57 0.25 0.16 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393228.22 0.61 0.23 0.13 0.03 0.16
## [7] 0.07 0.86 0.03 0.52 0.04
## [1] -392527.82 0.62 0.22 0.12 0.03 0.17
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -392307.96 0.63 0.22 0.12 0.04 0.17
## [7] 0.07 0.85 0.04 0.53 0.04
## [1] -392212.22 0.63 0.21 0.11 0.04 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392164.22 0.63 0.21 0.11 0.05 0.16
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392136.77 0.63 0.21 0.11 0.05 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -392117.62 0.63 0.20 0.11 0.06 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -392098.58 0.62 0.20 0.11 0.06 0.16
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -392075.68 0.62 0.20 0.11 0.07 0.16
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -392047.06 0.61 0.20 0.11 0.07 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -392012.25 0.60 0.20 0.11 0.08 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391971.56 0.60 0.21 0.12 0.08 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391925.96 0.59 0.21 0.12 0.08 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391876.63 0.59 0.21 0.12 0.09 0.15
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391825.04 0.58 0.21 0.12 0.09 0.15
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391772.23 0.57 0.21 0.12 0.10 0.15
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391719.71 0.57 0.21 0.12 0.10 0.15
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391668.19 0.56 0.21 0.12 0.10 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391618.50 0.55 0.21 0.13 0.11 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391571.22 0.55 0.21 0.13 0.11 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391526.75 0.54 0.22 0.13 0.12 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391485.32 0.53 0.22 0.13 0.12 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391447.05 0.52 0.22 0.13 0.13 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391411.95 0.52 0.22 0.13 0.13 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391379.97 0.51 0.22 0.13 0.14 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391351.01 0.50 0.22 0.13 0.14 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391324.93 0.50 0.22 0.14 0.14 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391301.57 0.49 0.22 0.14 0.15 0.15
## [7] 0.06 0.84 0.04 0.52 0.07
## [1] -391280.77 0.48 0.23 0.14 0.15 0.15
## [7] 0.06 0.84 0.04 0.52 0.07
## [1] -391262.36 0.47 0.23 0.14 0.16 0.15
## [7] 0.06 0.84 0.04 0.52 0.07
## [1] -391246.18 0.47 0.23 0.14 0.16 0.15
## [7] 0.06 0.84 0.04 0.52 0.07
## [1] -391232.08 0.46 0.23 0.14 0.17 0.15
## [7] 0.05 0.84 0.04 0.52 0.07
## [1] -391219.90 0.45 0.23 0.14 0.17 0.15
## [7] 0.05 0.84 0.04 0.52 0.08
## [1] -391209.51 0.45 0.23 0.14 0.18 0.15
## [7] 0.05 0.84 0.04 0.52 0.08
## [1] -391200.83 0.44 0.23 0.15 0.18 0.15
## [7] 0.05 0.84 0.04 0.52 0.08
## [1] 41
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401299.92 0.58 0.24 0.16 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393019.54 0.61 0.23 0.13 0.03 0.17
## [7] 0.07 0.86 0.03 0.52 0.04
## [1] -392273.34 0.63 0.21 0.12 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392032.83 0.64 0.21 0.12 0.04 0.17
## [7] 0.07 0.85 0.03 0.53 0.04
## [1] -391924.78 0.64 0.20 0.12 0.05 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -391870.43 0.64 0.20 0.11 0.05 0.17
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391840.92 0.63 0.20 0.11 0.06 0.17
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391822.46 0.63 0.20 0.11 0.06 0.16
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -391805.34 0.62 0.20 0.12 0.07 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391784.51 0.61 0.20 0.12 0.07 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391757.56 0.61 0.20 0.12 0.08 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391723.87 0.60 0.20 0.12 0.08 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391683.69 0.59 0.20 0.12 0.09 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391638.31 0.58 0.20 0.12 0.09 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391588.76 0.57 0.20 0.12 0.10 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391537.02 0.57 0.20 0.13 0.10 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391484.59 0.56 0.20 0.13 0.11 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391432.83 0.55 0.21 0.13 0.11 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391382.86 0.54 0.21 0.13 0.12 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391335.37 0.53 0.21 0.13 0.12 0.16
## [7] 0.06 0.83 0.04 0.54 0.06
## [1] -391290.96 0.53 0.21 0.13 0.13 0.15
## [7] 0.06 0.83 0.04 0.54 0.06
## [1] -391250.01 0.52 0.21 0.14 0.13 0.15
## [7] 0.06 0.83 0.04 0.54 0.06
## [1] -391212.68 0.51 0.21 0.14 0.14 0.15
## [7] 0.06 0.83 0.04 0.54 0.06
## [1] -391179.03 0.50 0.22 0.14 0.14 0.15
## [7] 0.06 0.83 0.04 0.53 0.06
## [1] -391148.98 0.49 0.22 0.14 0.15 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391122.42 0.48 0.22 0.14 0.16 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391099.15 0.47 0.22 0.14 0.16 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391078.99 0.47 0.22 0.14 0.17 0.15
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] -391061.73 0.46 0.22 0.15 0.17 0.15
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] -391047.15 0.45 0.23 0.15 0.18 0.15
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] -391035.12 0.44 0.23 0.15 0.18 0.15
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] -391025.34 0.43 0.23 0.15 0.19 0.15
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] 42
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400462.75 0.57 0.25 0.16 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393099.99 0.61 0.23 0.14 0.03 0.16
## [7] 0.07 0.86 0.03 0.52 0.04
## [1] -392431.12 0.62 0.22 0.12 0.03 0.16
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392211.50 0.63 0.21 0.12 0.04 0.16
## [7] 0.07 0.85 0.04 0.53 0.04
## [1] -392110.42 0.63 0.21 0.12 0.04 0.16
## [7] 0.07 0.85 0.04 0.53 0.04
## [1] -392057.18 0.63 0.21 0.11 0.05 0.16
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392025.77 0.63 0.20 0.11 0.05 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -392003.93 0.63 0.20 0.11 0.06 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391983.17 0.62 0.20 0.11 0.06 0.16
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -391959.17 0.62 0.20 0.12 0.07 0.16
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -391929.79 0.61 0.20 0.12 0.07 0.15
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -391894.34 0.60 0.20 0.12 0.08 0.15
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -391853.10 0.60 0.20 0.12 0.08 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391807.07 0.59 0.20 0.12 0.09 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391757.19 0.59 0.20 0.12 0.09 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391705.00 0.58 0.21 0.12 0.09 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391651.85 0.57 0.21 0.12 0.10 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391599.12 0.57 0.21 0.12 0.10 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391547.56 0.56 0.21 0.13 0.11 0.15
## [7] 0.06 0.84 0.04 0.54 0.06
## [1] -391498.05 0.55 0.21 0.13 0.11 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391451.20 0.55 0.21 0.13 0.12 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391407.43 0.54 0.21 0.13 0.12 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391366.98 0.53 0.21 0.13 0.12 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391329.96 0.52 0.21 0.13 0.13 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391296.39 0.52 0.22 0.13 0.13 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391266.20 0.51 0.22 0.13 0.14 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391239.26 0.50 0.22 0.14 0.14 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391215.42 0.49 0.22 0.14 0.15 0.14
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] -391194.51 0.49 0.22 0.14 0.15 0.14
## [7] 0.05 0.84 0.04 0.52 0.07
## [1] -391176.35 0.48 0.22 0.14 0.16 0.14
## [7] 0.05 0.84 0.04 0.52 0.07
## [1] -391160.74 0.47 0.22 0.14 0.16 0.14
## [7] 0.05 0.84 0.04 0.52 0.07
## [1] -391147.52 0.46 0.22 0.14 0.17 0.14
## [7] 0.05 0.84 0.04 0.52 0.08
## [1] -391136.51 0.46 0.23 0.14 0.17 0.14
## [7] 0.05 0.84 0.04 0.52 0.08
## [1] -391127.60 0.45 0.23 0.15 0.18 0.14
## [7] 0.05 0.84 0.04 0.52 0.08validation_epic.organoid$thresholded_ratio_max<-F
validation_epic.organoid$thresholded_ratio_max[which(validation_epic.organoid$thresholded_prior_ratio>1)]<-T
percent_passing<-round((tapply(validation_epic.organoid$thresholded_ratio_max, validation_epic.organoid$passage_hilo, sum)/tapply(validation_epic.organoid$array.id, validation_epic.organoid$passage_hilo, length))*100,2)
passed_num<-tapply(validation_epic.organoid$thresholded_ratio_max, validation_epic.organoid$passage_hilo, sum)
org_numer<-tapply(validation_epic.organoid$array.id, validation_epic.organoid$passage_hilo, length)
df<-data.frame(passage=names(percent_passing), passing=percent_passing, pro_passing=percent_passing/100, count=org_numer, passed_num=passed_num)
df<-cbind(df,(binom.confint(df$passed_num, df$count, method="exact", conf.level=0.95)))
df$upper<-df$upper*100
df$lower<-df$lower*100
print(df)## passage passing pro_passing count passed_num method x n mean
## high high 38.10 0.3810 21 8 exact 8 21 0.3809524
## low low 14.29 0.1429 21 3 exact 3 21 0.1428571
## lower upper
## high 18.107163 61.56456
## low 3.048897 36.34240Plot all samples
plts_paired<-lapply(1:nrow(validation_epic.organoid), function(x){#1:nrow(validation_epic.organoid)
print(x)
passage<-paste("passage: ",validation_epic.organoid$passage[x],"\nIndividual: ", validation_epic.organoid$Sample_Name[x],"\nRatio I/H: ",round(validation_epic.organoid$thresholded_prior_ratio[x],2), sep="")
converted<-as.numeric(round(validation_organoid_beta_VeryVariable[,x]*1000,0))
counts<-rep(1000, length(converted))
res = em(converted, counts, .41, .31, .27, 0.01, .1, .1, .90, .03, .5, .05)
draw_fit_params_gg(converted, counts, res,passage)
})## [1] 1
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -397515.94 0.55 0.25 0.18 0.02 0.15
## [7] 0.07 0.88 0.03 0.51 0.05
## [1] -391627.52 0.58 0.24 0.16 0.02 0.15
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -391311.14 0.60 0.22 0.15 0.03 0.15
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -391271.60 0.61 0.22 0.14 0.04 0.15
## [7] 0.06 0.87 0.03 0.52 0.04
## [1] -391279.02 0.61 0.21 0.13 0.04 0.15
## [7] 0.06 0.86 0.03 0.53 0.04
## [1] 2
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -397366.29 0.54 0.25 0.18 0.02 0.15
## [7] 0.07 0.88 0.03 0.51 0.05
## [1] -391640.40 0.58 0.24 0.16 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.04
## [1] -391333.52 0.60 0.23 0.15 0.03 0.15
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -391300.52 0.61 0.22 0.14 0.04 0.15
## [7] 0.06 0.87 0.03 0.52 0.04
## [1] -391314.51 0.61 0.21 0.14 0.04 0.15
## [7] 0.06 0.87 0.03 0.53 0.04
## [1] -391337.56 0.61 0.21 0.14 0.05 0.14
## [7] 0.06 0.87 0.03 0.53 0.04
## [1] -391359.52 0.61 0.20 0.13 0.05 0.14
## [7] 0.06 0.87 0.03 0.53 0.04
## [1] -391372.26 0.61 0.20 0.13 0.06 0.14
## [7] 0.05 0.87 0.03 0.53 0.04
## [1] -391373.64 0.61 0.20 0.13 0.06 0.14
## [7] 0.05 0.87 0.03 0.53 0.04
## [1] 3
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -399244.49 0.56 0.23 0.19 0.02 0.15
## [7] 0.08 0.88 0.03 0.51 0.05
## [1] -392243.87 0.59 0.21 0.17 0.02 0.16
## [7] 0.07 0.87 0.03 0.52 0.05
## [1] -391647.41 0.61 0.20 0.16 0.03 0.17
## [7] 0.07 0.86 0.03 0.53 0.04
## [1] -391483.96 0.62 0.19 0.16 0.03 0.17
## [7] 0.07 0.86 0.03 0.53 0.04
## [1] -391420.21 0.62 0.18 0.16 0.04 0.17
## [7] 0.07 0.86 0.03 0.54 0.04
## [1] -391392.00 0.62 0.18 0.16 0.04 0.17
## [7] 0.07 0.85 0.03 0.54 0.04
## [1] -391379.20 0.62 0.17 0.16 0.05 0.17
## [7] 0.07 0.85 0.03 0.54 0.04
## [1] -391372.70 0.62 0.17 0.16 0.05 0.16
## [7] 0.07 0.85 0.03 0.55 0.04
## [1] 4
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -398551.07 0.55 0.23 0.20 0.02 0.15
## [7] 0.07 0.88 0.03 0.51 0.05
## [1] -392065.62 0.59 0.21 0.18 0.02 0.16
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -391596.77 0.61 0.19 0.17 0.03 0.17
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -391474.81 0.62 0.19 0.16 0.04 0.17
## [7] 0.07 0.86 0.03 0.53 0.04
## [1] -391423.89 0.62 0.18 0.16 0.04 0.17
## [7] 0.07 0.86 0.03 0.54 0.04
## [1] -391395.66 0.62 0.18 0.16 0.04 0.17
## [7] 0.07 0.86 0.03 0.54 0.04
## [1] -391376.19 0.62 0.17 0.16 0.05 0.17
## [7] 0.07 0.86 0.03 0.54 0.04
## [1] -391359.68 0.62 0.17 0.16 0.05 0.16
## [7] 0.07 0.86 0.03 0.55 0.04
## [1] -391343.96 0.62 0.17 0.16 0.06 0.16
## [7] 0.07 0.86 0.03 0.55 0.04
## [1] -391325.61 0.61 0.17 0.16 0.06 0.16
## [7] 0.06 0.86 0.03 0.55 0.04
## [1] -391303.71 0.61 0.17 0.16 0.07 0.16
## [7] 0.06 0.86 0.03 0.55 0.04
## [1] -391277.80 0.60 0.17 0.16 0.07 0.16
## [7] 0.06 0.86 0.03 0.55 0.05
## [1] -391247.99 0.60 0.17 0.16 0.08 0.16
## [7] 0.06 0.86 0.03 0.55 0.05
## [1] -391214.76 0.59 0.17 0.16 0.08 0.16
## [7] 0.06 0.86 0.03 0.56 0.05
## [1] -391178.90 0.59 0.17 0.16 0.08 0.16
## [7] 0.06 0.86 0.03 0.56 0.05
## [1] -391141.28 0.58 0.17 0.16 0.09 0.15
## [7] 0.06 0.87 0.03 0.56 0.05
## [1] -391102.71 0.58 0.17 0.16 0.09 0.15
## [7] 0.06 0.87 0.03 0.56 0.05
## [1] -391064.15 0.57 0.17 0.16 0.10 0.15
## [7] 0.06 0.87 0.03 0.56 0.05
## [1] -391026.39 0.57 0.18 0.16 0.10 0.15
## [7] 0.06 0.87 0.03 0.56 0.06
## [1] -390990.11 0.56 0.18 0.16 0.10 0.15
## [7] 0.06 0.87 0.03 0.56 0.06
## [1] -390955.86 0.56 0.18 0.16 0.11 0.15
## [7] 0.06 0.87 0.03 0.56 0.06
## [1] -390924.08 0.55 0.18 0.16 0.11 0.15
## [7] 0.06 0.87 0.03 0.56 0.06
## [1] -390895.07 0.55 0.18 0.16 0.12 0.15
## [7] 0.06 0.87 0.03 0.56 0.06
## [1] -390869.01 0.54 0.18 0.16 0.12 0.15
## [7] 0.06 0.87 0.03 0.56 0.07
## [1] -390846.05 0.53 0.18 0.16 0.12 0.15
## [7] 0.06 0.87 0.03 0.56 0.07
## [1] -390826.23 0.53 0.18 0.16 0.13 0.15
## [7] 0.06 0.87 0.03 0.56 0.07
## [1] -390809.51 0.52 0.18 0.16 0.13 0.15
## [7] 0.06 0.87 0.03 0.56 0.07
## [1] -390795.83 0.52 0.18 0.16 0.14 0.15
## [7] 0.05 0.87 0.03 0.56 0.07
## [1] -390785.07 0.51 0.19 0.16 0.14 0.15
## [7] 0.05 0.87 0.03 0.56 0.08
## [1] -390777.10 0.50 0.19 0.16 0.15 0.15
## [7] 0.05 0.87 0.03 0.56 0.08
## [1] 5
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401736.10 0.57 0.26 0.15 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393400.10 0.61 0.24 0.12 0.03 0.16
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -392470.87 0.62 0.23 0.11 0.03 0.16
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392163.86 0.63 0.23 0.11 0.04 0.16
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392045.42 0.63 0.22 0.10 0.04 0.16
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392005.88 0.63 0.22 0.10 0.05 0.16
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391999.88 0.63 0.22 0.10 0.05 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] 6
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403181.16 0.59 0.25 0.14 0.02 0.16
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393624.52 0.62 0.24 0.11 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392548.39 0.64 0.23 0.10 0.03 0.17
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392184.71 0.64 0.22 0.09 0.04 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392038.21 0.64 0.22 0.09 0.05 0.17
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -391983.60 0.64 0.22 0.09 0.05 0.17
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391969.28 0.63 0.22 0.09 0.06 0.17
## [7] 0.06 0.81 0.04 0.54 0.04
## [1] -391968.67 0.62 0.22 0.09 0.07 0.17
## [7] 0.06 0.81 0.04 0.54 0.04
## [1] 7
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -404190.72 0.60 0.24 0.14 0.02 0.16
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393891.24 0.64 0.22 0.11 0.03 0.17
## [7] 0.07 0.84 0.03 0.52 0.04
## [1] -392563.39 0.65 0.21 0.11 0.04 0.18
## [7] 0.07 0.83 0.03 0.53 0.04
## [1] -392120.86 0.65 0.20 0.10 0.04 0.18
## [7] 0.07 0.82 0.03 0.53 0.04
## [1] -391966.08 0.65 0.20 0.10 0.05 0.18
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -391933.91 0.64 0.20 0.10 0.06 0.18
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -391953.46 0.64 0.20 0.10 0.06 0.18
## [7] 0.07 0.80 0.04 0.54 0.04
## [1] -391988.49 0.63 0.20 0.11 0.07 0.18
## [7] 0.07 0.80 0.04 0.55 0.04
## [1] -392018.66 0.62 0.20 0.11 0.08 0.18
## [7] 0.07 0.80 0.04 0.55 0.04
## [1] -392034.98 0.61 0.20 0.11 0.08 0.18
## [7] 0.07 0.79 0.04 0.55 0.04
## [1] -392034.36 0.59 0.21 0.11 0.09 0.18
## [7] 0.07 0.79 0.04 0.55 0.04
## [1] 8
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402715.66 0.58 0.24 0.15 0.02 0.16
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393422.88 0.62 0.23 0.13 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -392383.64 0.63 0.22 0.12 0.03 0.17
## [7] 0.07 0.84 0.03 0.53 0.04
## [1] -392049.59 0.64 0.21 0.12 0.04 0.18
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -391925.07 0.64 0.20 0.12 0.04 0.18
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391886.99 0.63 0.20 0.12 0.05 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -391886.54 0.63 0.20 0.12 0.05 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] 9
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401261.69 0.58 0.21 0.19 0.02 0.16
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -392806.79 0.62 0.18 0.17 0.03 0.18
## [7] 0.08 0.86 0.03 0.52 0.04
## [1] -391920.67 0.64 0.17 0.16 0.03 0.19
## [7] 0.08 0.85 0.03 0.53 0.04
## [1] -391632.83 0.65 0.16 0.16 0.04 0.19
## [7] 0.08 0.85 0.03 0.54 0.04
## [1] -391502.84 0.65 0.15 0.15 0.05 0.19
## [7] 0.08 0.84 0.03 0.54 0.04
## [1] -391434.58 0.64 0.15 0.15 0.06 0.19
## [7] 0.08 0.84 0.03 0.55 0.04
## [1] -391394.46 0.64 0.14 0.16 0.06 0.20
## [7] 0.08 0.84 0.03 0.55 0.04
## [1] -391367.24 0.63 0.14 0.16 0.07 0.20
## [7] 0.08 0.84 0.03 0.55 0.04
## [1] -391345.65 0.62 0.14 0.16 0.07 0.19
## [7] 0.08 0.84 0.03 0.55 0.04
## [1] -391324.99 0.62 0.15 0.16 0.08 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391303.07 0.61 0.15 0.16 0.08 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391279.08 0.60 0.15 0.16 0.09 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391252.94 0.59 0.15 0.16 0.09 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391224.95 0.58 0.15 0.17 0.10 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391195.57 0.57 0.16 0.17 0.10 0.19
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391165.37 0.56 0.16 0.17 0.11 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -391134.91 0.55 0.16 0.17 0.11 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -391105.88 0.54 0.16 0.17 0.12 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -391075.56 0.54 0.17 0.17 0.12 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -391046.95 0.53 0.17 0.18 0.13 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -391020.14 0.52 0.17 0.18 0.13 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -390995.03 0.51 0.18 0.18 0.14 0.19
## [7] 0.08 0.84 0.04 0.56 0.05
## [1] -390971.85 0.50 0.18 0.18 0.14 0.19
## [7] 0.08 0.84 0.03 0.56 0.05
## [1] -390950.61 0.49 0.18 0.18 0.15 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390931.35 0.48 0.18 0.18 0.15 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390914.09 0.47 0.19 0.18 0.16 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390898.81 0.46 0.19 0.19 0.16 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390885.44 0.45 0.19 0.19 0.17 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390873.91 0.44 0.19 0.19 0.17 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390863.90 0.44 0.20 0.19 0.18 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] -390855.79 0.43 0.20 0.19 0.18 0.19
## [7] 0.08 0.84 0.03 0.56 0.06
## [1] 10
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400720.44 0.58 0.20 0.20 0.02 0.17
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -392763.80 0.62 0.17 0.18 0.03 0.19
## [7] 0.08 0.87 0.03 0.52 0.04
## [1] -391942.07 0.64 0.15 0.17 0.04 0.20
## [7] 0.08 0.86 0.03 0.53 0.04
## [1] -391656.08 0.65 0.15 0.16 0.04 0.20
## [7] 0.08 0.86 0.03 0.53 0.04
## [1] -391516.99 0.65 0.14 0.16 0.05 0.21
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -391436.11 0.65 0.14 0.16 0.06 0.21
## [7] 0.08 0.85 0.04 0.55 0.04
## [1] -391381.68 0.64 0.13 0.16 0.06 0.21
## [7] 0.08 0.85 0.04 0.55 0.04
## [1] -391339.68 0.63 0.13 0.16 0.07 0.21
## [7] 0.08 0.85 0.04 0.55 0.04
## [1] -391303.39 0.63 0.13 0.17 0.07 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391270.19 0.62 0.14 0.17 0.08 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391237.85 0.61 0.14 0.17 0.08 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391205.97 0.60 0.14 0.17 0.09 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391174.14 0.59 0.14 0.17 0.09 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391143.01 0.59 0.14 0.17 0.10 0.21
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] -391112.14 0.58 0.15 0.17 0.10 0.21
## [7] 0.08 0.85 0.04 0.57 0.04
## [1] -391082.01 0.57 0.15 0.18 0.11 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -391052.94 0.56 0.15 0.18 0.11 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -391025.10 0.55 0.16 0.18 0.12 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390998.66 0.54 0.16 0.18 0.12 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390973.70 0.53 0.16 0.18 0.13 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390950.37 0.52 0.16 0.18 0.13 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390928.73 0.51 0.17 0.18 0.14 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390908.84 0.51 0.17 0.18 0.14 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390890.72 0.50 0.17 0.19 0.15 0.21
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390874.38 0.49 0.18 0.19 0.15 0.21
## [7] 0.08 0.85 0.04 0.57 0.06
## [1] -390859.78 0.48 0.18 0.19 0.15 0.21
## [7] 0.08 0.86 0.04 0.57 0.06
## [1] -390846.90 0.47 0.18 0.19 0.16 0.21
## [7] 0.08 0.86 0.04 0.57 0.06
## [1] -390835.69 0.46 0.18 0.19 0.17 0.21
## [7] 0.08 0.86 0.04 0.57 0.06
## [1] -390826.09 0.45 0.19 0.19 0.17 0.21
## [7] 0.08 0.86 0.03 0.57 0.06
## [1] 11
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400291.39 0.57 0.23 0.19 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -392644.37 0.61 0.21 0.16 0.03 0.17
## [7] 0.07 0.87 0.03 0.52 0.04
## [1] -392023.33 0.62 0.19 0.15 0.03 0.18
## [7] 0.07 0.86 0.03 0.52 0.04
## [1] -391857.40 0.63 0.19 0.15 0.04 0.18
## [7] 0.07 0.86 0.03 0.53 0.04
## [1] -391790.60 0.63 0.18 0.14 0.04 0.18
## [7] 0.07 0.85 0.03 0.53 0.04
## [1] -391754.53 0.63 0.18 0.14 0.05 0.18
## [7] 0.07 0.85 0.04 0.53 0.04
## [1] -391728.88 0.63 0.18 0.14 0.05 0.18
## [7] 0.07 0.85 0.04 0.54 0.04
## [1] -391705.90 0.62 0.17 0.14 0.06 0.18
## [7] 0.07 0.85 0.04 0.54 0.04
## [1] -391682.67 0.62 0.17 0.14 0.06 0.18
## [7] 0.07 0.85 0.04 0.54 0.04
## [1] -391656.61 0.61 0.17 0.15 0.07 0.18
## [7] 0.07 0.85 0.04 0.54 0.04
## [1] -391627.05 0.61 0.18 0.15 0.07 0.18
## [7] 0.07 0.85 0.04 0.54 0.04
## [1] -391594.02 0.60 0.18 0.15 0.08 0.18
## [7] 0.07 0.85 0.04 0.55 0.04
## [1] -391557.97 0.59 0.18 0.15 0.08 0.17
## [7] 0.07 0.85 0.04 0.55 0.04
## [1] -391519.20 0.59 0.18 0.15 0.08 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391478.70 0.58 0.18 0.15 0.09 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391436.85 0.57 0.18 0.15 0.09 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391395.22 0.57 0.18 0.15 0.10 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391353.56 0.56 0.18 0.16 0.10 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391313.67 0.55 0.19 0.16 0.11 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391275.93 0.54 0.19 0.16 0.11 0.17
## [7] 0.06 0.85 0.04 0.55 0.05
## [1] -391240.19 0.54 0.19 0.16 0.11 0.17
## [7] 0.06 0.85 0.04 0.55 0.06
## [1] -391206.76 0.53 0.19 0.16 0.12 0.17
## [7] 0.06 0.85 0.04 0.55 0.06
## [1] -391175.85 0.52 0.19 0.16 0.12 0.17
## [7] 0.06 0.85 0.04 0.54 0.06
## [1] -391147.56 0.51 0.20 0.16 0.13 0.17
## [7] 0.06 0.85 0.04 0.54 0.06
## [1] -391121.90 0.51 0.20 0.16 0.13 0.17
## [7] 0.06 0.85 0.04 0.54 0.06
## [1] -391098.86 0.50 0.20 0.16 0.14 0.17
## [7] 0.06 0.85 0.04 0.54 0.06
## [1] -391078.34 0.49 0.20 0.17 0.14 0.17
## [7] 0.06 0.85 0.04 0.54 0.06
## [1] -391058.86 0.48 0.20 0.17 0.15 0.17
## [7] 0.06 0.85 0.04 0.54 0.07
## [1] -391042.37 0.48 0.20 0.17 0.15 0.17
## [7] 0.06 0.85 0.04 0.54 0.07
## [1] -391028.36 0.47 0.21 0.17 0.16 0.17
## [7] 0.06 0.85 0.04 0.54 0.07
## [1] -391016.45 0.46 0.21 0.17 0.16 0.17
## [7] 0.06 0.85 0.04 0.54 0.07
## [1] -391004.70 0.45 0.21 0.17 0.17 0.17
## [7] 0.06 0.85 0.04 0.54 0.07
## [1] -390996.07 0.45 0.21 0.17 0.17 0.17
## [7] 0.06 0.86 0.04 0.54 0.07
## [1] 12
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400398.93 0.58 0.22 0.18 0.02 0.16
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -392994.09 0.61 0.20 0.16 0.03 0.17
## [7] 0.08 0.86 0.03 0.52 0.04
## [1] -392346.60 0.63 0.19 0.15 0.03 0.18
## [7] 0.08 0.86 0.03 0.52 0.04
## [1] -392164.50 0.64 0.18 0.14 0.04 0.18
## [7] 0.08 0.85 0.03 0.53 0.04
## [1] -392090.16 0.64 0.17 0.14 0.05 0.18
## [7] 0.08 0.85 0.03 0.53 0.04
## [1] -392050.33 0.64 0.17 0.14 0.05 0.19
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -392022.23 0.64 0.17 0.14 0.06 0.19
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -391997.27 0.63 0.17 0.14 0.06 0.18
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -391972.55 0.63 0.17 0.14 0.07 0.18
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -391945.82 0.62 0.17 0.14 0.07 0.18
## [7] 0.08 0.85 0.04 0.54 0.04
## [1] -391916.61 0.61 0.17 0.14 0.08 0.18
## [7] 0.08 0.85 0.04 0.55 0.04
## [1] -391884.90 0.61 0.17 0.14 0.08 0.18
## [7] 0.08 0.85 0.04 0.55 0.04
## [1] -391851.37 0.60 0.17 0.14 0.09 0.18
## [7] 0.07 0.85 0.04 0.55 0.04
## [1] -391815.84 0.59 0.17 0.15 0.09 0.18
## [7] 0.07 0.85 0.04 0.55 0.04
## [1] -391779.28 0.58 0.17 0.15 0.09 0.18
## [7] 0.07 0.85 0.04 0.55 0.04
## [1] -391741.62 0.58 0.18 0.15 0.10 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391704.48 0.57 0.18 0.15 0.10 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391666.96 0.56 0.18 0.15 0.11 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391631.57 0.55 0.18 0.15 0.11 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391598.07 0.55 0.18 0.15 0.12 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391566.28 0.54 0.19 0.15 0.12 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391536.59 0.53 0.19 0.16 0.13 0.18
## [7] 0.07 0.85 0.04 0.55 0.05
## [1] -391509.12 0.52 0.19 0.16 0.13 0.18
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391483.96 0.52 0.19 0.16 0.13 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391461.14 0.51 0.19 0.16 0.14 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391440.66 0.50 0.20 0.16 0.14 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391422.48 0.49 0.20 0.16 0.15 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391406.56 0.48 0.20 0.16 0.15 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391392.80 0.48 0.20 0.16 0.16 0.17
## [7] 0.07 0.85 0.04 0.55 0.06
## [1] -391381.12 0.47 0.20 0.17 0.16 0.17
## [7] 0.07 0.85 0.04 0.55 0.07
## [1] -391371.06 0.46 0.20 0.17 0.17 0.17
## [7] 0.07 0.85 0.04 0.55 0.07
## [1] -391360.75 0.45 0.21 0.17 0.17 0.17
## [7] 0.07 0.85 0.04 0.54 0.07
## [1] -391353.90 0.44 0.21 0.17 0.18 0.17
## [7] 0.07 0.85 0.04 0.54 0.07
## [1] 13
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403138.89 0.59 0.23 0.16 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -393726.11 0.63 0.20 0.14 0.03 0.17
## [7] 0.08 0.85 0.03 0.52 0.05
## [1] -392454.83 0.65 0.19 0.13 0.03 0.18
## [7] 0.08 0.83 0.03 0.53 0.04
## [1] -392029.12 0.65 0.18 0.13 0.04 0.18
## [7] 0.08 0.83 0.04 0.54 0.04
## [1] -391881.03 0.65 0.18 0.13 0.05 0.18
## [7] 0.08 0.82 0.04 0.54 0.04
## [1] -391849.05 0.65 0.17 0.13 0.05 0.18
## [7] 0.08 0.82 0.04 0.54 0.04
## [1] -391863.32 0.64 0.17 0.13 0.06 0.18
## [7] 0.08 0.81 0.04 0.55 0.04
## [1] -391889.93 0.63 0.17 0.13 0.06 0.18
## [7] 0.07 0.81 0.04 0.55 0.04
## [1] -391911.78 0.62 0.17 0.13 0.07 0.18
## [7] 0.07 0.81 0.04 0.55 0.04
## [1] -391921.40 0.61 0.17 0.14 0.07 0.18
## [7] 0.07 0.81 0.04 0.55 0.04
## [1] 14
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403611.87 0.60 0.22 0.16 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -393996.17 0.64 0.20 0.13 0.03 0.18
## [7] 0.08 0.85 0.03 0.52 0.04
## [1] -392661.94 0.65 0.19 0.12 0.04 0.18
## [7] 0.08 0.83 0.04 0.53 0.04
## [1] -392206.40 0.66 0.18 0.12 0.04 0.19
## [7] 0.08 0.83 0.04 0.53 0.04
## [1] -392045.57 0.66 0.17 0.12 0.05 0.19
## [7] 0.08 0.82 0.04 0.54 0.04
## [1] -392008.21 0.65 0.17 0.12 0.06 0.19
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] -392020.53 0.64 0.17 0.12 0.06 0.19
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] -392046.43 0.64 0.17 0.13 0.07 0.19
## [7] 0.08 0.81 0.04 0.55 0.04
## [1] -392067.83 0.63 0.17 0.13 0.07 0.19
## [7] 0.08 0.80 0.04 0.55 0.04
## [1] -392077.62 0.62 0.17 0.13 0.08 0.19
## [7] 0.08 0.80 0.04 0.55 0.04
## [1] 15
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403588.34 0.60 0.24 0.14 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -394220.97 0.64 0.22 0.12 0.03 0.18
## [7] 0.08 0.85 0.03 0.52 0.04
## [1] -393021.13 0.65 0.20 0.11 0.04 0.18
## [7] 0.08 0.83 0.04 0.52 0.04
## [1] -392593.88 0.66 0.20 0.10 0.04 0.19
## [7] 0.08 0.83 0.04 0.53 0.04
## [1] -392423.11 0.66 0.19 0.10 0.05 0.19
## [7] 0.08 0.82 0.04 0.53 0.04
## [1] -392365.42 0.65 0.19 0.10 0.06 0.19
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] -392358.77 0.65 0.19 0.10 0.06 0.19
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] 16
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403501.55 0.60 0.23 0.15 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -394218.47 0.64 0.21 0.12 0.03 0.18
## [7] 0.08 0.85 0.03 0.52 0.04
## [1] -393033.25 0.65 0.20 0.11 0.04 0.19
## [7] 0.08 0.84 0.04 0.52 0.04
## [1] -392617.32 0.66 0.19 0.10 0.04 0.19
## [7] 0.08 0.83 0.04 0.53 0.04
## [1] -392452.85 0.66 0.19 0.10 0.05 0.19
## [7] 0.08 0.82 0.04 0.53 0.04
## [1] -392398.02 0.65 0.19 0.10 0.06 0.19
## [7] 0.08 0.82 0.04 0.54 0.04
## [1] -392392.35 0.65 0.19 0.10 0.06 0.19
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] 17
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -399928.06 0.57 0.19 0.22 0.02 0.16
## [7] 0.09 0.87 0.03 0.51 0.05
## [1] -392356.74 0.61 0.15 0.21 0.03 0.18
## [7] 0.09 0.86 0.03 0.53 0.05
## [1] -391316.08 0.63 0.14 0.20 0.03 0.19
## [7] 0.09 0.85 0.03 0.54 0.04
## [1] -390938.56 0.63 0.12 0.20 0.04 0.20
## [7] 0.10 0.85 0.03 0.54 0.04
## [1] -390775.20 0.63 0.12 0.20 0.04 0.20
## [7] 0.10 0.85 0.03 0.55 0.04
## [1] -390704.67 0.63 0.11 0.21 0.05 0.20
## [7] 0.10 0.84 0.04 0.56 0.04
## [1] -390676.38 0.63 0.11 0.21 0.05 0.21
## [7] 0.10 0.84 0.04 0.56 0.04
## [1] -390665.19 0.62 0.11 0.21 0.06 0.21
## [7] 0.10 0.84 0.04 0.56 0.04
## [1] -390658.34 0.61 0.11 0.21 0.06 0.21
## [7] 0.10 0.84 0.04 0.56 0.04
## [1] 18
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -398969.63 0.57 0.18 0.23 0.02 0.16
## [7] 0.09 0.87 0.03 0.51 0.05
## [1] -392350.42 0.61 0.15 0.22 0.03 0.18
## [7] 0.09 0.86 0.03 0.53 0.04
## [1] -391393.38 0.63 0.13 0.21 0.03 0.19
## [7] 0.10 0.86 0.03 0.54 0.04
## [1] -391026.20 0.63 0.12 0.21 0.04 0.20
## [7] 0.10 0.85 0.03 0.54 0.04
## [1] -390857.04 0.63 0.11 0.21 0.04 0.20
## [7] 0.11 0.85 0.04 0.55 0.04
## [1] -390775.81 0.63 0.11 0.21 0.05 0.20
## [7] 0.11 0.85 0.04 0.56 0.04
## [1] -390735.21 0.63 0.11 0.21 0.05 0.21
## [7] 0.11 0.85 0.04 0.56 0.04
## [1] -390711.63 0.62 0.10 0.21 0.06 0.21
## [7] 0.11 0.85 0.04 0.56 0.04
## [1] -390692.85 0.62 0.10 0.22 0.06 0.21
## [7] 0.11 0.85 0.04 0.56 0.04
## [1] -390673.80 0.61 0.10 0.22 0.07 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390651.64 0.61 0.10 0.22 0.07 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390625.77 0.60 0.11 0.22 0.07 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390596.83 0.59 0.11 0.22 0.08 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390565.71 0.59 0.11 0.22 0.08 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390533.05 0.58 0.11 0.22 0.09 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390499.48 0.58 0.11 0.22 0.09 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390465.59 0.57 0.11 0.22 0.09 0.21
## [7] 0.11 0.85 0.04 0.57 0.04
## [1] -390431.78 0.56 0.12 0.23 0.10 0.20
## [7] 0.11 0.85 0.04 0.58 0.05
## [1] -390398.38 0.56 0.12 0.23 0.10 0.20
## [7] 0.11 0.85 0.04 0.58 0.05
## [1] -390365.66 0.55 0.12 0.23 0.10 0.20
## [7] 0.11 0.85 0.04 0.58 0.05
## [1] -390333.75 0.55 0.12 0.23 0.11 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390302.78 0.54 0.12 0.23 0.11 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390272.89 0.53 0.13 0.23 0.11 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390244.14 0.53 0.13 0.23 0.12 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390216.59 0.52 0.13 0.23 0.12 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390190.28 0.51 0.13 0.23 0.12 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390165.23 0.51 0.13 0.23 0.13 0.20
## [7] 0.10 0.85 0.04 0.58 0.05
## [1] -390141.49 0.50 0.14 0.23 0.13 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390118.97 0.50 0.14 0.23 0.13 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390097.75 0.49 0.14 0.23 0.14 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390077.78 0.48 0.14 0.23 0.14 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390059.02 0.48 0.14 0.23 0.14 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390041.47 0.47 0.15 0.23 0.15 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390025.10 0.46 0.15 0.24 0.15 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -390009.88 0.46 0.15 0.24 0.16 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -389995.77 0.45 0.15 0.24 0.16 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -389982.74 0.45 0.15 0.24 0.16 0.20
## [7] 0.10 0.85 0.04 0.58 0.06
## [1] -389970.76 0.44 0.16 0.24 0.17 0.20
## [7] 0.10 0.85 0.04 0.58 0.07
## [1] -389959.79 0.43 0.16 0.24 0.17 0.20
## [7] 0.10 0.85 0.04 0.58 0.07
## [1] -389949.80 0.43 0.16 0.24 0.17 0.20
## [7] 0.10 0.85 0.04 0.58 0.07
## [1] 19
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -399597.90 0.57 0.21 0.21 0.02 0.16
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -392507.68 0.61 0.18 0.19 0.03 0.17
## [7] 0.08 0.86 0.03 0.52 0.05
## [1] -391710.23 0.62 0.16 0.18 0.03 0.18
## [7] 0.08 0.86 0.03 0.53 0.04
## [1] -391450.54 0.63 0.15 0.18 0.04 0.18
## [7] 0.08 0.85 0.03 0.54 0.04
## [1] -391342.43 0.63 0.15 0.18 0.04 0.18
## [7] 0.09 0.85 0.03 0.54 0.04
## [1] -391295.44 0.63 0.14 0.18 0.05 0.19
## [7] 0.09 0.85 0.03 0.55 0.04
## [1] -391276.18 0.63 0.14 0.18 0.05 0.19
## [7] 0.09 0.85 0.04 0.55 0.04
## [1] -391269.00 0.62 0.14 0.18 0.06 0.18
## [7] 0.08 0.85 0.04 0.56 0.04
## [1] 20
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400914.74 0.58 0.20 0.20 0.02 0.16
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -392712.31 0.62 0.18 0.18 0.03 0.18
## [7] 0.08 0.86 0.03 0.52 0.04
## [1] -391819.32 0.63 0.16 0.17 0.03 0.19
## [7] 0.08 0.85 0.03 0.53 0.04
## [1] -391531.20 0.64 0.15 0.17 0.04 0.19
## [7] 0.08 0.85 0.03 0.54 0.04
## [1] -391407.01 0.64 0.15 0.17 0.05 0.20
## [7] 0.08 0.85 0.03 0.54 0.04
## [1] -391347.36 0.64 0.14 0.17 0.05 0.20
## [7] 0.08 0.85 0.03 0.55 0.04
## [1] -391316.93 0.63 0.14 0.17 0.06 0.20
## [7] 0.08 0.84 0.03 0.55 0.04
## [1] -391299.60 0.63 0.14 0.17 0.06 0.20
## [7] 0.08 0.84 0.03 0.56 0.04
## [1] -391287.10 0.62 0.14 0.17 0.07 0.20
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391275.59 0.61 0.14 0.17 0.07 0.20
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391262.07 0.61 0.15 0.17 0.08 0.20
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391245.40 0.60 0.15 0.17 0.08 0.20
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391225.64 0.59 0.15 0.18 0.09 0.20
## [7] 0.08 0.84 0.04 0.56 0.04
## [1] -391203.00 0.58 0.15 0.18 0.09 0.20
## [7] 0.08 0.84 0.04 0.57 0.04
## [1] -391177.94 0.57 0.15 0.18 0.09 0.20
## [7] 0.08 0.84 0.04 0.57 0.04
## [1] -391152.52 0.57 0.16 0.18 0.10 0.20
## [7] 0.08 0.84 0.04 0.57 0.04
## [1] -391123.76 0.56 0.16 0.18 0.10 0.20
## [7] 0.08 0.84 0.04 0.57 0.04
## [1] -391094.77 0.55 0.16 0.18 0.11 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -391065.76 0.54 0.17 0.18 0.11 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -391037.17 0.53 0.17 0.19 0.11 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -391009.32 0.52 0.17 0.19 0.12 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -390982.50 0.52 0.17 0.19 0.12 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -390956.89 0.51 0.18 0.19 0.13 0.20
## [7] 0.08 0.84 0.04 0.57 0.05
## [1] -390932.64 0.50 0.18 0.19 0.13 0.20
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390909.87 0.49 0.18 0.19 0.14 0.20
## [7] 0.08 0.85 0.04 0.57 0.05
## [1] -390888.60 0.48 0.19 0.19 0.14 0.20
## [7] 0.08 0.85 0.03 0.57 0.05
## [1] -390868.86 0.47 0.19 0.19 0.14 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390850.63 0.47 0.19 0.19 0.15 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390833.89 0.46 0.19 0.20 0.15 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390818.59 0.45 0.20 0.20 0.16 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390804.67 0.44 0.20 0.20 0.16 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390792.09 0.43 0.20 0.20 0.17 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390780.76 0.42 0.20 0.20 0.17 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390770.64 0.42 0.21 0.20 0.18 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] -390761.67 0.41 0.21 0.20 0.18 0.20
## [7] 0.08 0.85 0.03 0.57 0.06
## [1] 21
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403647.99 0.60 0.24 0.14 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -393801.07 0.64 0.22 0.12 0.03 0.17
## [7] 0.08 0.84 0.03 0.52 0.04
## [1] -392537.71 0.65 0.21 0.11 0.04 0.18
## [7] 0.08 0.83 0.03 0.53 0.04
## [1] -392095.16 0.65 0.20 0.10 0.04 0.18
## [7] 0.08 0.82 0.03 0.53 0.04
## [1] -391922.77 0.65 0.19 0.10 0.05 0.18
## [7] 0.08 0.81 0.03 0.54 0.04
## [1] -391869.92 0.65 0.19 0.10 0.06 0.18
## [7] 0.08 0.81 0.04 0.54 0.04
## [1] -391870.44 0.64 0.19 0.11 0.07 0.18
## [7] 0.08 0.80 0.04 0.54 0.04
## [1] 22
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402847.53 0.59 0.24 0.15 0.02 0.16
## [7] 0.08 0.86 0.03 0.51 0.05
## [1] -393886.15 0.63 0.22 0.12 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392760.66 0.64 0.21 0.11 0.03 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392377.06 0.65 0.20 0.11 0.04 0.18
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392231.32 0.65 0.20 0.11 0.05 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392186.68 0.64 0.19 0.11 0.05 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392185.73 0.64 0.19 0.11 0.06 0.18
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] 23
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402801.75 0.59 0.23 0.16 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393639.57 0.63 0.21 0.14 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -392551.37 0.64 0.20 0.13 0.03 0.18
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392180.72 0.65 0.19 0.12 0.04 0.18
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392033.78 0.65 0.19 0.12 0.05 0.18
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391983.12 0.64 0.19 0.12 0.05 0.18
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391975.93 0.64 0.18 0.12 0.06 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] 24
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -404177.72 0.60 0.23 0.15 0.02 0.17
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -394036.85 0.64 0.21 0.12 0.03 0.18
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -392802.68 0.65 0.20 0.11 0.04 0.19
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392371.97 0.66 0.20 0.10 0.04 0.20
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392191.99 0.65 0.19 0.10 0.05 0.20
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392121.30 0.65 0.19 0.10 0.06 0.20
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392101.50 0.64 0.19 0.10 0.06 0.20
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -392102.06 0.63 0.19 0.10 0.07 0.20
## [7] 0.07 0.81 0.05 0.54 0.04
## [1] 25
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -404482.56 0.61 0.23 0.14 0.02 0.17
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393990.92 0.64 0.21 0.12 0.03 0.18
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392686.41 0.66 0.20 0.11 0.04 0.19
## [7] 0.07 0.83 0.03 0.52 0.04
## [1] -392220.64 0.66 0.19 0.10 0.05 0.19
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392024.59 0.66 0.19 0.10 0.05 0.20
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -391949.61 0.65 0.19 0.10 0.06 0.20
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -391931.37 0.64 0.19 0.10 0.07 0.20
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -391935.15 0.63 0.19 0.10 0.08 0.20
## [7] 0.07 0.80 0.04 0.54 0.04
## [1] 26
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402869.78 0.59 0.26 0.14 0.02 0.15
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393897.60 0.62 0.24 0.11 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -392820.30 0.64 0.23 0.10 0.03 0.17
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392440.62 0.64 0.22 0.10 0.04 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392283.37 0.64 0.22 0.09 0.05 0.17
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392225.56 0.64 0.22 0.09 0.05 0.17
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392214.34 0.63 0.22 0.09 0.06 0.17
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -392221.30 0.63 0.22 0.10 0.06 0.17
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] 27
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403547.91 0.59 0.25 0.14 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393838.80 0.63 0.23 0.11 0.03 0.18
## [7] 0.07 0.85 0.03 0.51 0.04
## [1] -392779.46 0.64 0.22 0.10 0.03 0.18
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392404.66 0.65 0.22 0.10 0.04 0.18
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392235.20 0.65 0.21 0.09 0.05 0.18
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392157.19 0.64 0.21 0.09 0.05 0.18
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392124.18 0.64 0.21 0.09 0.06 0.18
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392111.11 0.63 0.21 0.09 0.07 0.18
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -392103.47 0.62 0.21 0.10 0.07 0.18
## [7] 0.07 0.81 0.05 0.54 0.04
## [1] 28
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403985.93 0.60 0.25 0.14 0.02 0.16
## [7] 0.07 0.86 0.03 0.51 0.05
## [1] -393904.32 0.63 0.23 0.11 0.03 0.18
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392759.65 0.64 0.22 0.10 0.03 0.18
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392357.65 0.65 0.22 0.09 0.04 0.19
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392183.66 0.65 0.21 0.09 0.05 0.19
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392111.90 0.64 0.21 0.09 0.06 0.19
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392090.00 0.64 0.21 0.09 0.06 0.19
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] -392089.45 0.63 0.21 0.09 0.07 0.19
## [7] 0.07 0.81 0.04 0.54 0.04
## [1] 29
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402127.58 0.58 0.25 0.15 0.02 0.15
## [7] 0.08 0.87 0.03 0.51 0.05
## [1] -393953.50 0.62 0.24 0.12 0.03 0.17
## [7] 0.07 0.85 0.04 0.52 0.05
## [1] -392980.52 0.64 0.22 0.11 0.03 0.17
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392629.74 0.64 0.22 0.10 0.04 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392477.38 0.64 0.21 0.10 0.05 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392413.92 0.64 0.21 0.10 0.05 0.17
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392392.53 0.64 0.21 0.10 0.06 0.17
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -392388.13 0.63 0.21 0.10 0.06 0.17
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] 30
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403506.10 0.60 0.24 0.14 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -394385.31 0.63 0.22 0.11 0.03 0.18
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -393241.12 0.65 0.21 0.10 0.04 0.18
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392817.30 0.65 0.21 0.10 0.04 0.19
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392632.00 0.65 0.20 0.09 0.05 0.19
## [7] 0.07 0.82 0.04 0.53 0.04
## [1] -392557.26 0.65 0.20 0.09 0.06 0.19
## [7] 0.07 0.82 0.05 0.54 0.04
## [1] -392536.92 0.65 0.20 0.09 0.06 0.19
## [7] 0.07 0.81 0.05 0.54 0.04
## [1] -392540.01 0.64 0.20 0.09 0.07 0.19
## [7] 0.07 0.81 0.05 0.54 0.04
## [1] 31
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403240.20 0.59 0.23 0.16 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393403.63 0.63 0.21 0.14 0.03 0.18
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -392255.93 0.64 0.19 0.13 0.03 0.18
## [7] 0.07 0.84 0.03 0.53 0.04
## [1] -391885.38 0.64 0.19 0.13 0.04 0.19
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -391746.01 0.64 0.18 0.13 0.05 0.19
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391699.79 0.64 0.18 0.13 0.05 0.19
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] -391693.22 0.63 0.18 0.13 0.06 0.19
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] 32
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402911.87 0.59 0.23 0.17 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393714.80 0.62 0.21 0.14 0.03 0.18
## [7] 0.07 0.85 0.04 0.52 0.05
## [1] -392592.72 0.64 0.19 0.13 0.03 0.18
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392230.87 0.65 0.19 0.13 0.04 0.19
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392097.95 0.65 0.18 0.13 0.04 0.19
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392055.26 0.64 0.18 0.13 0.05 0.19
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -392049.02 0.64 0.18 0.13 0.05 0.19
## [7] 0.07 0.82 0.04 0.54 0.04
## [1] 33
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -403904.05 0.59 0.20 0.18 0.02 0.18
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393101.84 0.63 0.19 0.16 0.03 0.20
## [7] 0.06 0.86 0.04 0.51 0.05
## [1] -391934.01 0.64 0.18 0.15 0.03 0.21
## [7] 0.06 0.85 0.04 0.52 0.05
## [1] -391592.67 0.64 0.18 0.14 0.04 0.22
## [7] 0.06 0.85 0.04 0.52 0.05
## [1] -391470.08 0.64 0.18 0.14 0.04 0.22
## [7] 0.06 0.84 0.04 0.53 0.04
## [1] -391426.83 0.63 0.18 0.14 0.05 0.22
## [7] 0.06 0.84 0.04 0.53 0.04
## [1] -391416.24 0.63 0.18 0.15 0.05 0.22
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391418.69 0.62 0.18 0.15 0.06 0.22
## [7] 0.06 0.83 0.05 0.54 0.04
## [1] 34
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401732.65 0.57 0.26 0.15 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393375.68 0.61 0.24 0.12 0.03 0.16
## [7] 0.07 0.85 0.03 0.51 0.04
## [1] -392550.12 0.63 0.23 0.11 0.03 0.17
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -392288.08 0.63 0.22 0.11 0.04 0.17
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392178.39 0.63 0.22 0.10 0.04 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392127.30 0.63 0.22 0.10 0.05 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392100.32 0.63 0.22 0.10 0.05 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -392081.06 0.62 0.21 0.10 0.06 0.16
## [7] 0.06 0.83 0.04 0.53 0.04
## [1] -392061.05 0.62 0.21 0.10 0.06 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -392035.34 0.61 0.22 0.10 0.07 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] -392002.17 0.60 0.22 0.11 0.07 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] -391961.38 0.60 0.22 0.11 0.08 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391913.76 0.59 0.22 0.11 0.08 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391860.69 0.58 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.05
## [1] -391803.96 0.58 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.05
## [1] -391744.88 0.57 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.05
## [1] -391685.00 0.56 0.22 0.12 0.10 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391625.54 0.55 0.22 0.12 0.10 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391567.42 0.55 0.23 0.12 0.11 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391511.57 0.54 0.23 0.12 0.11 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391458.00 0.53 0.23 0.12 0.12 0.16
## [7] 0.06 0.82 0.05 0.53 0.06
## [1] -391407.30 0.52 0.23 0.12 0.12 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391359.62 0.52 0.23 0.13 0.12 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391314.99 0.51 0.23 0.13 0.13 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391273.38 0.50 0.24 0.13 0.13 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391234.68 0.49 0.24 0.13 0.14 0.15
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391198.76 0.49 0.24 0.13 0.14 0.15
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391165.49 0.48 0.24 0.14 0.15 0.15
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391134.70 0.47 0.24 0.14 0.15 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391106.23 0.46 0.24 0.14 0.16 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391079.92 0.45 0.24 0.14 0.16 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391055.63 0.45 0.25 0.14 0.17 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391033.23 0.44 0.25 0.15 0.17 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391012.57 0.43 0.25 0.15 0.18 0.15
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -390993.55 0.42 0.25 0.15 0.18 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -390976.05 0.41 0.25 0.15 0.18 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -390959.97 0.41 0.25 0.15 0.19 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390945.22 0.40 0.25 0.15 0.19 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390931.72 0.39 0.25 0.16 0.20 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390919.39 0.38 0.25 0.16 0.20 0.15
## [7] 0.05 0.82 0.05 0.50 0.08
## [1] -390908.16 0.38 0.26 0.16 0.21 0.15
## [7] 0.05 0.82 0.05 0.50 0.08
## [1] -390897.97 0.37 0.26 0.16 0.21 0.15
## [7] 0.05 0.82 0.05 0.50 0.08
## [1] -390888.75 0.36 0.26 0.16 0.22 0.15
## [7] 0.05 0.82 0.05 0.50 0.08
## [1] 35
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401850.66 0.57 0.25 0.16 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393221.70 0.61 0.23 0.13 0.03 0.17
## [7] 0.07 0.86 0.03 0.52 0.05
## [1] -392372.99 0.62 0.22 0.12 0.03 0.17
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -392119.38 0.63 0.22 0.12 0.04 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392022.92 0.63 0.21 0.12 0.04 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -391985.13 0.63 0.21 0.11 0.05 0.17
## [7] 0.07 0.83 0.04 0.53 0.04
## [1] -391970.90 0.63 0.21 0.11 0.05 0.17
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391964.31 0.62 0.21 0.12 0.06 0.17
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] 36
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401823.48 0.57 0.25 0.15 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393352.60 0.61 0.24 0.12 0.03 0.17
## [7] 0.07 0.86 0.04 0.51 0.04
## [1] -392519.40 0.62 0.23 0.11 0.03 0.17
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -392268.86 0.63 0.23 0.11 0.04 0.17
## [7] 0.07 0.84 0.04 0.52 0.04
## [1] -392172.95 0.63 0.22 0.10 0.04 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392134.47 0.63 0.22 0.10 0.05 0.17
## [7] 0.06 0.83 0.04 0.53 0.04
## [1] -392118.38 0.63 0.22 0.10 0.05 0.17
## [7] 0.06 0.83 0.04 0.53 0.04
## [1] -392108.20 0.62 0.22 0.10 0.06 0.17
## [7] 0.06 0.83 0.04 0.53 0.04
## [1] -392095.12 0.62 0.22 0.10 0.06 0.17
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -392074.93 0.61 0.22 0.11 0.07 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] -392046.15 0.60 0.22 0.11 0.07 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] -392008.87 0.60 0.22 0.11 0.08 0.16
## [7] 0.06 0.82 0.04 0.54 0.04
## [1] -391964.11 0.59 0.22 0.11 0.08 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391913.38 0.58 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391858.64 0.58 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.04
## [1] -391801.12 0.57 0.22 0.11 0.09 0.16
## [7] 0.06 0.82 0.04 0.53 0.05
## [1] -391742.47 0.56 0.22 0.12 0.10 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391683.95 0.55 0.23 0.12 0.10 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391626.52 0.55 0.23 0.12 0.11 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391571.13 0.54 0.23 0.12 0.11 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391517.83 0.53 0.23 0.12 0.11 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391467.22 0.52 0.23 0.13 0.12 0.16
## [7] 0.06 0.82 0.05 0.53 0.05
## [1] -391419.47 0.52 0.23 0.13 0.12 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391374.65 0.51 0.24 0.13 0.13 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391332.73 0.50 0.24 0.13 0.13 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391293.63 0.49 0.24 0.13 0.13 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391257.24 0.49 0.24 0.13 0.14 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391223.42 0.48 0.24 0.14 0.14 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391192.01 0.47 0.24 0.14 0.15 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391162.88 0.46 0.25 0.14 0.15 0.16
## [7] 0.06 0.82 0.05 0.52 0.06
## [1] -391135.87 0.46 0.25 0.14 0.16 0.16
## [7] 0.06 0.82 0.05 0.52 0.07
## [1] -391110.84 0.45 0.25 0.14 0.16 0.16
## [7] 0.06 0.82 0.05 0.52 0.07
## [1] -391087.66 0.44 0.25 0.15 0.16 0.16
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391066.18 0.43 0.25 0.15 0.17 0.16
## [7] 0.06 0.82 0.05 0.51 0.07
## [1] -391046.31 0.43 0.25 0.15 0.17 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -391027.93 0.42 0.25 0.15 0.18 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -391010.93 0.41 0.25 0.15 0.18 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -390995.24 0.40 0.26 0.15 0.19 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -390980.76 0.40 0.26 0.16 0.19 0.15
## [7] 0.05 0.82 0.05 0.51 0.07
## [1] -390967.43 0.39 0.26 0.16 0.20 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390955.16 0.38 0.26 0.16 0.20 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390943.90 0.37 0.26 0.16 0.21 0.15
## [7] 0.05 0.82 0.05 0.51 0.08
## [1] -390933.58 0.37 0.26 0.16 0.21 0.15
## [7] 0.05 0.83 0.05 0.51 0.08
## [1] -390924.16 0.36 0.26 0.16 0.21 0.15
## [7] 0.05 0.83 0.05 0.51 0.08
## [1] 37
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401646.97 0.58 0.23 0.17 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -392856.08 0.61 0.21 0.15 0.03 0.17
## [7] 0.07 0.86 0.03 0.52 0.05
## [1] -391939.60 0.63 0.20 0.14 0.03 0.17
## [7] 0.07 0.85 0.03 0.53 0.04
## [1] -391634.20 0.63 0.19 0.14 0.04 0.17
## [7] 0.07 0.84 0.03 0.53 0.04
## [1] -391506.99 0.63 0.18 0.14 0.04 0.17
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391455.22 0.63 0.18 0.14 0.05 0.17
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391438.02 0.63 0.18 0.14 0.05 0.17
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391434.36 0.62 0.18 0.14 0.06 0.17
## [7] 0.07 0.83 0.04 0.55 0.04
## [1] 38
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -402091.04 0.58 0.23 0.17 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -392947.65 0.62 0.21 0.14 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.05
## [1] -391982.95 0.63 0.20 0.14 0.03 0.17
## [7] 0.07 0.84 0.03 0.53 0.04
## [1] -391665.86 0.64 0.19 0.13 0.04 0.17
## [7] 0.07 0.84 0.03 0.53 0.04
## [1] -391536.11 0.64 0.19 0.13 0.04 0.17
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391485.04 0.63 0.18 0.13 0.05 0.17
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391469.83 0.63 0.18 0.13 0.06 0.17
## [7] 0.07 0.83 0.04 0.54 0.04
## [1] -391468.32 0.62 0.18 0.14 0.06 0.17
## [7] 0.07 0.83 0.04 0.55 0.04
## [1] 39
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400190.16 0.56 0.24 0.18 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -392404.48 0.59 0.22 0.16 0.02 0.16
## [7] 0.07 0.86 0.03 0.52 0.05
## [1] -391577.56 0.61 0.21 0.16 0.03 0.16
## [7] 0.07 0.85 0.03 0.53 0.05
## [1] -391319.07 0.62 0.20 0.15 0.03 0.16
## [7] 0.07 0.85 0.03 0.54 0.04
## [1] -391227.25 0.62 0.19 0.15 0.04 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391205.47 0.62 0.19 0.15 0.04 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391214.81 0.61 0.19 0.15 0.05 0.15
## [7] 0.06 0.84 0.04 0.55 0.04
## [1] 40
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400741.31 0.57 0.25 0.16 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393228.22 0.61 0.23 0.13 0.03 0.16
## [7] 0.07 0.86 0.03 0.52 0.04
## [1] -392527.82 0.62 0.22 0.12 0.03 0.17
## [7] 0.07 0.85 0.04 0.52 0.04
## [1] -392307.96 0.63 0.22 0.12 0.04 0.17
## [7] 0.07 0.85 0.04 0.53 0.04
## [1] -392212.22 0.63 0.21 0.11 0.04 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392164.22 0.63 0.21 0.11 0.05 0.16
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392136.77 0.63 0.21 0.11 0.05 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -392117.62 0.63 0.20 0.11 0.06 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -392098.58 0.62 0.20 0.11 0.06 0.16
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -392075.68 0.62 0.20 0.11 0.07 0.16
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -392047.06 0.61 0.20 0.11 0.07 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -392012.25 0.60 0.20 0.11 0.08 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391971.56 0.60 0.21 0.12 0.08 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391925.96 0.59 0.21 0.12 0.08 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391876.63 0.59 0.21 0.12 0.09 0.15
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391825.04 0.58 0.21 0.12 0.09 0.15
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391772.23 0.57 0.21 0.12 0.10 0.15
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391719.71 0.57 0.21 0.12 0.10 0.15
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391668.19 0.56 0.21 0.12 0.10 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391618.50 0.55 0.21 0.13 0.11 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391571.22 0.55 0.21 0.13 0.11 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391526.75 0.54 0.22 0.13 0.12 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391485.32 0.53 0.22 0.13 0.12 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391447.05 0.52 0.22 0.13 0.13 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391411.95 0.52 0.22 0.13 0.13 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391379.97 0.51 0.22 0.13 0.14 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391351.01 0.50 0.22 0.13 0.14 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391324.93 0.50 0.22 0.14 0.14 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391301.57 0.49 0.22 0.14 0.15 0.15
## [7] 0.06 0.84 0.04 0.52 0.07
## [1] -391280.77 0.48 0.23 0.14 0.15 0.15
## [7] 0.06 0.84 0.04 0.52 0.07
## [1] -391262.36 0.47 0.23 0.14 0.16 0.15
## [7] 0.06 0.84 0.04 0.52 0.07
## [1] -391246.18 0.47 0.23 0.14 0.16 0.15
## [7] 0.06 0.84 0.04 0.52 0.07
## [1] -391232.08 0.46 0.23 0.14 0.17 0.15
## [7] 0.05 0.84 0.04 0.52 0.07
## [1] -391219.90 0.45 0.23 0.14 0.17 0.15
## [7] 0.05 0.84 0.04 0.52 0.08
## [1] -391209.51 0.45 0.23 0.14 0.18 0.15
## [7] 0.05 0.84 0.04 0.52 0.08
## [1] -391200.83 0.44 0.23 0.15 0.18 0.15
## [7] 0.05 0.84 0.04 0.52 0.08
## [1] 41
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -401299.92 0.58 0.24 0.16 0.02 0.16
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393019.54 0.61 0.23 0.13 0.03 0.17
## [7] 0.07 0.86 0.03 0.52 0.04
## [1] -392273.34 0.63 0.21 0.12 0.03 0.17
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392032.83 0.64 0.21 0.12 0.04 0.17
## [7] 0.07 0.85 0.03 0.53 0.04
## [1] -391924.78 0.64 0.20 0.12 0.05 0.17
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -391870.43 0.64 0.20 0.11 0.05 0.17
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391840.92 0.63 0.20 0.11 0.06 0.17
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391822.46 0.63 0.20 0.11 0.06 0.16
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -391805.34 0.62 0.20 0.12 0.07 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391784.51 0.61 0.20 0.12 0.07 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391757.56 0.61 0.20 0.12 0.08 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391723.87 0.60 0.20 0.12 0.08 0.16
## [7] 0.06 0.83 0.04 0.54 0.04
## [1] -391683.69 0.59 0.20 0.12 0.09 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391638.31 0.58 0.20 0.12 0.09 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391588.76 0.57 0.20 0.12 0.10 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391537.02 0.57 0.20 0.13 0.10 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391484.59 0.56 0.20 0.13 0.11 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391432.83 0.55 0.21 0.13 0.11 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391382.86 0.54 0.21 0.13 0.12 0.16
## [7] 0.06 0.83 0.04 0.54 0.05
## [1] -391335.37 0.53 0.21 0.13 0.12 0.16
## [7] 0.06 0.83 0.04 0.54 0.06
## [1] -391290.96 0.53 0.21 0.13 0.13 0.15
## [7] 0.06 0.83 0.04 0.54 0.06
## [1] -391250.01 0.52 0.21 0.14 0.13 0.15
## [7] 0.06 0.83 0.04 0.54 0.06
## [1] -391212.68 0.51 0.21 0.14 0.14 0.15
## [7] 0.06 0.83 0.04 0.54 0.06
## [1] -391179.03 0.50 0.22 0.14 0.14 0.15
## [7] 0.06 0.83 0.04 0.53 0.06
## [1] -391148.98 0.49 0.22 0.14 0.15 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391122.42 0.48 0.22 0.14 0.16 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391099.15 0.47 0.22 0.14 0.16 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391078.99 0.47 0.22 0.14 0.17 0.15
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] -391061.73 0.46 0.22 0.15 0.17 0.15
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] -391047.15 0.45 0.23 0.15 0.18 0.15
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] -391035.12 0.44 0.23 0.15 0.18 0.15
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] -391025.34 0.43 0.23 0.15 0.19 0.15
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] 42
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -400462.75 0.57 0.25 0.16 0.02 0.15
## [7] 0.07 0.87 0.03 0.51 0.05
## [1] -393099.99 0.61 0.23 0.14 0.03 0.16
## [7] 0.07 0.86 0.03 0.52 0.04
## [1] -392431.12 0.62 0.22 0.12 0.03 0.16
## [7] 0.07 0.85 0.03 0.52 0.04
## [1] -392211.50 0.63 0.21 0.12 0.04 0.16
## [7] 0.07 0.85 0.04 0.53 0.04
## [1] -392110.42 0.63 0.21 0.12 0.04 0.16
## [7] 0.07 0.85 0.04 0.53 0.04
## [1] -392057.18 0.63 0.21 0.11 0.05 0.16
## [7] 0.07 0.84 0.04 0.53 0.04
## [1] -392025.77 0.63 0.20 0.11 0.05 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -392003.93 0.63 0.20 0.11 0.06 0.16
## [7] 0.07 0.84 0.04 0.54 0.04
## [1] -391983.17 0.62 0.20 0.11 0.06 0.16
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -391959.17 0.62 0.20 0.12 0.07 0.16
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -391929.79 0.61 0.20 0.12 0.07 0.15
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -391894.34 0.60 0.20 0.12 0.08 0.15
## [7] 0.06 0.84 0.04 0.54 0.04
## [1] -391853.10 0.60 0.20 0.12 0.08 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391807.07 0.59 0.20 0.12 0.09 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391757.19 0.59 0.20 0.12 0.09 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391705.00 0.58 0.21 0.12 0.09 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391651.85 0.57 0.21 0.12 0.10 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391599.12 0.57 0.21 0.12 0.10 0.15
## [7] 0.06 0.84 0.04 0.54 0.05
## [1] -391547.56 0.56 0.21 0.13 0.11 0.15
## [7] 0.06 0.84 0.04 0.54 0.06
## [1] -391498.05 0.55 0.21 0.13 0.11 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391451.20 0.55 0.21 0.13 0.12 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391407.43 0.54 0.21 0.13 0.12 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391366.98 0.53 0.21 0.13 0.12 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391329.96 0.52 0.21 0.13 0.13 0.15
## [7] 0.06 0.84 0.04 0.53 0.06
## [1] -391296.39 0.52 0.22 0.13 0.13 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391266.20 0.51 0.22 0.13 0.14 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391239.26 0.50 0.22 0.14 0.14 0.15
## [7] 0.06 0.84 0.04 0.53 0.07
## [1] -391215.42 0.49 0.22 0.14 0.15 0.14
## [7] 0.05 0.84 0.04 0.53 0.07
## [1] -391194.51 0.49 0.22 0.14 0.15 0.14
## [7] 0.05 0.84 0.04 0.52 0.07
## [1] -391176.35 0.48 0.22 0.14 0.16 0.14
## [7] 0.05 0.84 0.04 0.52 0.07
## [1] -391160.74 0.47 0.22 0.14 0.16 0.14
## [7] 0.05 0.84 0.04 0.52 0.07
## [1] -391147.52 0.46 0.22 0.14 0.17 0.14
## [7] 0.05 0.84 0.04 0.52 0.08
## [1] -391136.51 0.46 0.23 0.14 0.17 0.14
## [7] 0.05 0.84 0.04 0.52 0.08
## [1] -391127.60 0.45 0.23 0.15 0.18 0.14
## [7] 0.05 0.84 0.04 0.52 0.08plts_paired_order<-plts_paired[order(validation_epic.organoid$passage)]
pdf(here("figs","validation_organoids_thresholding_all_samples.pdf"))
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## 2###############Differential methylation with passage
###############Only in UT UD
validation_epic.organoid_UT_UD<-validation_epic.organoid[which(validation_epic.organoid$differentiation=="UD" & validation_epic.organoid$treatment=="UT"),]
table(validation_epic.organoid_UT_UD$passage_hilo)##
## high low
## 9 9validation_organoid_beta_UT_UD<-validation_organoid_beta[,which(colnames(validation_organoid_beta)%in%validation_epic.organoid_UT_UD$array.id)]
identical(validation_epic.organoid_UT_UD$array.id, colnames(validation_organoid_beta_UT_UD))## [1] TRUEmod<-model.matrix(~ 0 + passage + individual, data=validation_epic.organoid_UT_UD)
fit <- lmFit(validation_organoid_beta_UT_UD, mod)
ebfit <- eBayes(fit)
# covariate adjusted beta values
passage_db<-sapply(1:nrow(validation_organoid_beta), function(x){
sampleinfo_cpg<-validation_epic.organoid
sampleinfo_cpg$beta<-as.numeric(validation_organoid_beta[x,])
fit<-lm(beta ~ passage + individual, data=sampleinfo_cpg)
pval<-summary(fit)$coef["passage","Pr(>|t|)"]
slope<-fit$coefficients[2]
(min(validation_epic.organoid$passage)*slope) - (max(validation_epic.organoid$passage)*slope)})
passage_validation<-data.frame(p.value=ebfit$p.value[,"passage"], CpG=rownames(validation_organoid_beta), db=passage_db)
# Adjust P values
passage_validation$p_adjusted<-p.adjust(passage_validation$p.value, method="BH")
diff_CpG_dbvalidation<-passage_validation[which(passage_validation$p_adjusted<0.05 & abs(passage_validation$db)>0.15),] #19746
diff_CpG_db_hypovalidation<-diff_CpG_dbvalidation$CpG[which((diff_CpG_dbvalidation$db)>=0.15)] # 19221
diff_CpG_db_hypervalidation<-diff_CpG_dbvalidation$CpG[which((diff_CpG_dbvalidation$db)<=(-0.15))] # 525load original organoid passage CpGs
load(here("data","beta_organoids.RData"))
pvals_long<-read.csv(here("data","Heteroskedactiy_pvalues_FDR_1000iter.csv"), header=T)
pvals_long[,1]<-NULL
colnames(pvals_long)<-c("BP_count","diff_count","mean_db","fdr_BP","fdr_diff")
pvals_long$CpG<-rownames(organoid_beta)
pvals_long$BP_pval<-((1000-pvals_long$BP_count)+1)/1001
pvals_long$diff_pval<-((1000-pvals_long$diff_count)+1)/1001
pvals_long$BP_fdr<-((1000-pvals_long$fdr_BP)+1)/1001
pvals_long$diff_fdr<-((1000-pvals_long$fdr_diff)+1)/1001
hetero_CpG<-rownames(organoid_beta)[which(pvals_long$BP_fdr<0.05)]
print(paste("CpGs with significant (adjusted p<0.05) heteroskedactiy: ", length(hetero_CpG), sep=""))## [1] "CpGs with significant (adjusted p<0.05) heteroskedactiy: 41852"diff_CpG<-rownames(organoid_beta)[which(pvals_long$diff_fdr<0.05)]
diff_CpG_db<-pvals_long[which(pvals_long$diff_fdr<0.05 & abs(pvals_long$mean_db)>0.15),]
print(paste("CpGs with significant (adjusted p<0.05; delta beta >0.05) differential methylation: ", nrow(diff_CpG_db), sep=""))## [1] "CpGs with significant (adjusted p<0.05; delta beta >0.05) differential methylation: 23766"diff_CpG_db_hypo<-diff_CpG_db$CpG[which((diff_CpG_db$mean_db)>=0.15)] # 11772
diff_CpG_db_hyper<-diff_CpG_db$CpG[which((diff_CpG_db$mean_db)<=(-0.15))] # 5214How many differential CpGs could overlap? 450K vs EPIC
print(paste("Of the ", nrow(diff_CpG_db), " CpGs differential with passage in the original organoids, ",
length(diff_CpG_db$CpG[which(diff_CpG_db$CpG%in%rownames(validation_organoid_beta))]), " are in the validation data", sep=""))## [1] "Of the 23766 CpGs differential with passage in the original organoids, 23737 are in the validation data"diff_CpG_db_hypo_overlap<-diff_CpG_db_hypo[which(diff_CpG_db_hypo%in%rownames(validation_organoid_beta))]
diff_CpG_db_hyper_overlap<-diff_CpG_db_hyper[which(diff_CpG_db_hyper%in%rownames(validation_organoid_beta))]
diff_CpG_db_hypovalidation_overlap<-diff_CpG_db_hypovalidation[which(diff_CpG_db_hypovalidation%in%pvals_long$CpG)]
diff_CpG_db_hypervalidation_overlap<-diff_CpG_db_hypervalidation[which(diff_CpG_db_hypervalidation%in%pvals_long$CpG)]
print(paste("Of the ",length(diff_CpG_db_hypo_overlap)," hypo CpGs also on the 450K ",
length(intersect(diff_CpG_db_hypovalidation_overlap, diff_CpG_db_hypo_overlap))," are also hypo in the validation cohort (",
round((length(intersect(diff_CpG_db_hypovalidation_overlap, diff_CpG_db_hypo_overlap))/length(diff_CpG_db_hypo_overlap))*100,2),"%)",sep=""))## [1] "Of the 17327 hypo CpGs also on the 450K 9349 are also hypo in the validation cohort (53.96%)"print(paste("Of the ",length(diff_CpG_db_hyper_overlap)," hypo CpGs also on the 450K ",
length(intersect(diff_CpG_db_hypervalidation_overlap, diff_CpG_db_hyper_overlap))," are also hypo in the validation cohort (",
round((length(intersect(diff_CpG_db_hypervalidation_overlap, diff_CpG_db_hyper_overlap))/length(diff_CpG_db_hyper_overlap))*100,2),"%)",sep=""))## [1] "Of the 6410 hypo CpGs also on the 450K 457 are also hypo in the validation cohort (7.13%)"delta beta directionality plot
plt_db_direction<-merge(pvals_long[,c(3,6)], passage_validation, by="CpG")# 380776
plt_db_direction$sig<-"Not Significant"
plt_db_direction$sig[which(plt_db_direction$CpG%in%c(intersect(diff_CpG_db_hypovalidation_overlap, diff_CpG_db_hypo_overlap),intersect(diff_CpG_db_hypervalidation_overlap, diff_CpG_db_hyper_overlap)))]<-"Significant\nIn Both\nCohorts"
ggplot(plt_db_direction, aes(mean_db, db))+geom_point(aes(color=sig, alpha=sig),shape=19)+th+theme_bw()+
scale_color_manual(values=c("lightgrey", "cornflowerblue"), name="Significant\nWith Passage")+
scale_alpha_manual(values=c(0.25,1), guide=F)+
geom_hline(yintercept=c(-0.15,0.15), color="grey60")+geom_vline(xintercept=c(-0.15,0.15), color="grey60")+
ylim(-0.9,0.9)+xlim(-0.9,0.9)+xlab("Cohort 1 Organoid\nPassage Delta Beta")+ylab("Validation Organoid\nPassage Delta Beta")+
stat_smooth(method="lm", se=F, color="black")
#ggsave(here("figs","validation_db_directionality.pdf"), width=5, height=3.75)
ggsave(here("figs/jpeg","validation_db_directionality.jpeg"), width=5, height=3.75)
print(paste("Correlation of delta betas between cohorts: ", round(cor(plt_db_direction$db, plt_db_direction$mean_db),2), sep=""))## [1] "Correlation of delta betas between cohorts: 0.67"representative CpGs
epic.organoid_minimal<-epic.organoid[,c(2, 14, 17)]
colnames(epic.organoid_minimal)[1]<-"Assay.Name"
epic.organoid_minimal$cohort<-"Cohort 1 Organoids"
validation_epic.organoid_UT_UD$Sample_ID<-paste(validation_epic.organoid_UT_UD$individual, validation_epic.organoid_UT_UD$Segment, validation_epic.organoid_UT_UD$condition)
validation_epic.organoid_minimal<-validation_epic.organoid_UT_UD[,c(10, 19, 12)]
colnames(validation_epic.organoid_minimal)[1]<-"Assay.Name"
validation_epic.organoid_minimal$cohort<-"Validation Organoids"
colnames(validation_epic.organoid_minimal)[2:3]<-c("sample_ID","passage.or.rescope.no_numeric")
sample_info_both<-rbind(validation_epic.organoid_minimal,epic.organoid_minimal)
sample_info_both$passage.or.rescope.no_numeric<-as.numeric(as.character(sample_info_both$passage.or.rescope.no_numeric))
plt_hetero_validation<-function(CpGs, legend, axislab, title){
betas<-melt(cbind(validation_organoid_beta_UT_UD[CpGs,],organoid_beta[CpGs,]))
organoid_plt<-merge(sample_info_both, betas, by.x="Assay.Name",by.y="Var2")
p<-ggplot(organoid_plt, aes(passage.or.rescope.no_numeric,value))+
geom_line(aes(group=sample_ID),color="lightgrey")+
stat_smooth(method="lm", color="grey30", size=0.7, se=F)+th+theme_bw()+
geom_point(aes(fill=as.factor(passage.or.rescope.no_numeric)),shape=21, size=1.25)+
scale_fill_manual(values=pass_col,name="Passage\nNumber", drop=T)+
facet_grid(cohort~Var1)+
ylab("DNAm Beta")+xlab("Passage Number")+ylim(0,1)+
theme(plot.margin = margin(0.5, 0.15, 0.5, 0.15, "cm"),plot.title = element_text(size=12))+
xlim(1,16)
if(missing(legend) & missing(axislab) & missing(title)){p}else{
if(legend=="N" & axislab=="N"){p + theme(legend.position = "none",axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())+ ggtitle(title)}else{
if(legend=="N" & axislab=="Y"){p + theme(legend.position = "none") + ggtitle(title)}}}}
plt_hetero_validation(c("cg25402228","cg22009751"))## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?## Warning: Removed 10 rows containing missing values (geom_smooth).
ggsave(here("figs","Passage_differential_CpGs_validation.pdf"),width = 4.75, height = 4)## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?## Warning: Removed 10 rows containing missing values (geom_smooth).ggsave(here("figs/jpeg","Passage_differential_CpGs_validation.jpeg"), width = 4.75, height = 4)## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?## Warning: Removed 10 rows containing missing values (geom_smooth).CpG to gene associations
EPIC_genes<-read.csv(here("data","EPIC_ensembl_gene_annotation.csv")) # 1137194
diff_genes_db_hypovalidation<-unique(EPIC_genes$Gene.name[which(EPIC_genes$IlmnID%in%diff_CpG_db_hypovalidation)] ) #8365
diff_genes_db_hypervalidation<-unique(EPIC_genes$Gene.name[which(EPIC_genes$IlmnID%in%diff_CpG_db_hypervalidation)] ) # 454
write.table(diff_genes_db_hypovalidation, file=here("data/validation/DNAm/","validation_genes_hypomethylation_UTUD.txt"), quote=F, row.names = F, col.names = F)
write.table(diff_genes_db_hypervalidation, file=here("data/validation/DNAm/","validation_genes_hypermethylation_UTUD.txt"), quote=F, row.names = F, col.names = F)Genes differential in original and validation
diff_genes_db_hypovalidation_original<-unique(EPIC_genes$Gene.name[which(EPIC_genes$IlmnID%in%intersect(diff_CpG_db_hypovalidation_overlap, diff_CpG_db_hypo_overlap))] ) # 4722
diff_genes_db_hypervalidation_original<-unique(EPIC_genes$Gene.name[which(EPIC_genes$IlmnID%in%intersect(diff_CpG_db_hypervalidation_overlap, diff_CpG_db_hyper_overlap))] ) # 402
write.table(diff_genes_db_hypovalidation_original, file=here("data/validation/DNAm/","validation_original_genes_hypomethylation_UTUD.txt"), quote=F, row.names = F, col.names = F)
write.table(diff_genes_db_hypervalidation_original, file=here("data/validation/DNAm/","validation_original_genes_hypermethylation_UTUD.txt"), quote=F, row.names = F, col.names = F)DNAm plot of differenitally expressed genes
gene_DNAm<-function(gene){
CpG_goi<-EPIC_genes[which(EPIC_genes$Gene.name%in%gene),]
CpG_gene<-CpG_goi[which(CpG_goi$IlmnID%in%c(diff_CpG_db_hypovalidation_overlap, diff_CpG_db_hypervalidation_overlap)),]
CpGs<-unique(CpG_gene$IlmnID)
CpG_gene<-CpG_gene[!duplicated(CpG_gene[,c(3,7)]), c(3,7)]
CpG_gene$label<-paste(CpG_gene$IlmnID, "\n(",CpG_gene$Gene.name, ")", sep="")
betas<-melt(cbind(validation_organoid_beta_UT_UD[CpGs,],organoid_beta[CpGs,]))
organoid_plt<-merge(sample_info_both, betas, by.x="Assay.Name",by.y="Var2")
organoid_plt<-merge(organoid_plt, CpG_gene, by.x="Var1",by.y="IlmnID")
ggplot(organoid_plt, aes(passage.or.rescope.no_numeric,value))+
geom_line(aes(group=sample_ID),color="lightgrey")+
stat_smooth(method="lm", color="grey30", size=0.7, se=F)+th+theme_bw()+
geom_point(aes(fill=as.factor(passage.or.rescope.no_numeric)),shape=21, size=1.25)+
scale_fill_manual(values=pass_col,name="Passage\nNumber", drop=T)+
facet_grid(cohort~label)+
ylab("DNAm Beta")+xlab("Passage Number")+ylim(0,1)+
theme(plot.margin = margin(0.5, 0.15, 0.5, 0.15, "cm"),plot.title = element_text(size=12))+
xlim(1,16)
}
gene_DNAm(c("EDAR","RNASE4","EIF4G1","LRRC59"))## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
ggsave(here("figs","validation_differenital_DNAm_passage.pdf"),width = 9, height = 4)## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?ggsave(here("figs/jpeg","validation_differenital_DNAm_passage.jpeg"), width = 9, height = 4)## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?R Session Info
sessionInfo()## R version 3.5.1 (2018-07-02)
## Platform: x86_64-conda_cos6-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux Server 7.4 (Maipo)
##
## Matrix products: default
## BLAS/LAPACK: /homes/redgar/anaconda3/envs/org_pass/lib/R/lib/libRblas.so
##
## locale:
## [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
## [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
## [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] splines stats4 parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
## [2] IlluminaHumanMethylationEPICmanifest_0.3.0
## [3] VGAM_1.1-1
## [4] reshape2_1.4.3
## [5] scales_1.0.0
## [6] rafalib_1.0.0
## [7] gtools_3.8.1
## [8] lmtest_0.9-37
## [9] zoo_1.8-4
## [10] dplyr_0.8.0.1
## [11] GEOmetadb_1.44.0
## [12] RSQLite_2.1.1
## [13] GEOquery_2.50.0
## [14] pamr_1.56
## [15] survival_2.43-3
## [16] cluster_2.0.7-1
## [17] sva_3.30.0
## [18] genefilter_1.64.0
## [19] mgcv_1.8-26
## [20] nlme_3.1-137
## [21] limma_3.38.3
## [22] binom_1.1-1
## [23] here_0.1
## [24] RColorBrewer_1.1-2
## [25] gridExtra_2.3
## [26] ggplot2_3.1.0
## [27] reshape_0.8.8
## [28] minfi_1.28.0
## [29] bumphunter_1.24.5
## [30] locfit_1.5-9.1
## [31] iterators_1.0.10
## [32] foreach_1.4.4
## [33] Biostrings_2.50.1
## [34] XVector_0.22.0
## [35] SummarizedExperiment_1.12.0
## [36] DelayedArray_0.8.0
## [37] BiocParallel_1.16.2
## [38] matrixStats_0.54.0
## [39] Biobase_2.42.0
## [40] GenomicRanges_1.34.0
## [41] GenomeInfoDb_1.18.1
## [42] IRanges_2.16.0
## [43] S4Vectors_0.20.1
## [44] BiocGenerics_0.28.0
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.4-0 siggenes_1.56.0
## [3] mclust_5.4.2 rprojroot_1.3-2
## [5] base64_2.0 bit64_0.9-7
## [7] AnnotationDbi_1.44.0 xml2_1.2.0
## [9] codetools_0.2-16 knitr_1.21
## [11] Rsamtools_1.34.0 annotate_1.60.0
## [13] HDF5Array_1.10.1 readr_1.3.1
## [15] compiler_3.5.1 httr_1.4.0
## [17] backports_1.1.3 assertthat_0.2.0
## [19] Matrix_1.2-15 lazyeval_0.2.1
## [21] htmltools_0.3.6 prettyunits_1.0.2
## [23] tools_3.5.1 gtable_0.2.0
## [25] glue_1.3.0 GenomeInfoDbData_1.2.0
## [27] doRNG_1.7.1 Rcpp_1.0.0
## [29] multtest_2.38.0 preprocessCore_1.44.0
## [31] rtracklayer_1.42.2 DelayedMatrixStats_1.4.0
## [33] xfun_0.4 stringr_1.4.0
## [35] rngtools_1.3.1 XML_3.98-1.16
## [37] beanplot_1.2 zlibbioc_1.28.0
## [39] MASS_7.3-51.1 hms_0.4.2
## [41] rhdf5_2.26.2 yaml_2.2.0
## [43] memoise_1.1.0 pkgmaker_0.27
## [45] biomaRt_2.38.0 stringi_1.2.4
## [47] highr_0.7 GenomicFeatures_1.34.1
## [49] bibtex_0.4.2 rlang_0.3.1
## [51] pkgconfig_2.0.2 bitops_1.0-6
## [53] nor1mix_1.2-3 evaluate_0.12
## [55] lattice_0.20-38 purrr_0.2.5
## [57] Rhdf5lib_1.4.2 labeling_0.3
## [59] GenomicAlignments_1.18.0 bit_1.1-12
## [61] tidyselect_0.2.5 plyr_1.8.4
## [63] magrittr_1.5 R6_2.4.0
## [65] DBI_1.0.0 pillar_1.4.3
## [67] withr_2.1.2 RCurl_1.95-4.11
## [69] tibble_2.0.1 crayon_1.3.4
## [71] rmarkdown_1.11 progress_1.2.0
## [73] grid_3.5.1 data.table_1.12.0
## [75] blob_1.1.1 digest_0.6.18
## [77] xtable_1.8-2 tidyr_0.8.2
## [79] illuminaio_0.24.0 openssl_1.1
## [81] munsell_0.5.0 registry_0.5
## [83] quadprog_1.5-5